Merge branch 'master' into update-crabs

bioconda · Oct 24, 2024 · c785fa3 · c785fa3
2 parents 3adf5b9 + 11b7dce
commit c785fa3
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -9,7 +9,7 @@ executors:
   linux-aarch64:
     machine:
       image: ubuntu-2204:current
-    resource_class: arm.medium
+    resource_class: arm.large
 
 jobs: # a basic unit of work in a run
   build_and_test:

diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -772,9 +772,6 @@ recipes/perl-gd
 # sha mismatch when downloading source
 recipes/fmlrc2
 
-# tries to download zlib itself, which fails
-recipes/d4binding
-
 # no matching package named `quickersort` found
 recipes/mudskipper
 

diff --git a/recipes/abismal/build.sh b/recipes/abismal/build.sh
@@ -1,4 +1,9 @@
 #!/bin/bash
-./configure --prefix=$PREFIX
-make CXXFLAGS="-O3 -D_LIBCPP_DISABLE_AVAILABILITY"
+
+export M4="${BUILD_PREFIX}/bin/m4"
+
+autoreconf -if
+./configure --prefix="$PREFIX"
+
+make CXXFLAGS="${CXXFLAGS} -O3 -D_LIBCPP_DISABLE_AVAILABILITY"
 make install
diff --git a/recipes/abismal/meta.yaml b/recipes/abismal/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "3.2.3" %}
+{% set version = "3.2.4" %}
 
 package:
   name: abismal
@@ -10,32 +10,36 @@ build:
     # abismal is currently not intended to be stable between minor versions (x.x).
     - {{ pin_subpackage('abismal', max_pin="x.x") }}
 
-
 source:
   url: https://github.com/smithlabcode/abismal/releases/download/v{{ version }}/abismal-{{ version }}.tar.gz
-  sha256: 0698ca408feb7e2650468e66dfdd4615e9405f64cd5496272fe2226cefd21322
+  sha256: 822e5efe322f989c561a1fb728bd6f57f49d94033620eb1bc5046f22a8492544
 
 requirements:
   build:
     - make
     - {{ compiler('cxx') }}
     - autoconf
     - automake
-    - llvm-openmp  # [osx]
-    - libgomp      # [linux]
+    - libtool
   host:
     - zlib
     - htslib
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
   run:
     - htslib
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
 
 about:
-  home: https://github.com/smithlabcode/abismal
-  license: GPL-3.0-only
+  home: "https://github.com/smithlabcode/abismal"
+  license: "GPL-3.0-only"
+  license_family: GPL3
   license_file: LICENSE
   summary: |
-    abismal is a fast and memory-efficient mapper for short bisulfite sequencing reads
-  doc_url: 'https://github.com/smithlabcode/abismal/blob/master/docs/MANUAL.md'
+    abismal is a fast and memory-efficient mapper for short bisulfite sequencing reads.
+  doc_url: 'https://github.com/smithlabcode/abismal/blob/v{{ version }}/docs/MANUAL.md'
+  dev_url: "https://github.com/smithlabcode/abismal"
 
 test:
   commands:
@@ -45,3 +49,6 @@ extra:
   recipe-maintainers:
     - andrewdavidsmith
     - guilhermesena1
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/abyss/build.sh b/recipes/abyss/build.sh
@@ -1,5 +1,8 @@
 #!/bin/bash
 
+export M4="${BUILD_PREFIX}/bin/m4"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+
 if [[ "$(uname)" == Darwin ]]; then
     # Fix for install_name_tool error:
     #   error: install_name_tool: changing install names or rpaths can't be
@@ -9,13 +12,14 @@ if [[ "$(uname)" == Darwin ]]; then
     export LDFLAGS="$LDFLAGS -headerpad_max_install_names"
 fi
 
-./configure \
-    --prefix="$PREFIX" \
-    --with-boost="$PREFIX" \
-    --with-mpi="$PREFIX" \
-    --with-sparsehash="$PREFIX" \
-    --without-sqlite || cat config.log
-make AM_CXXFLAGS=-Wall
+autoreconf -if
+./configure --prefix="${PREFIX}" \
+	CXXFLAGS="${CXXFLAGS} -std=c++14 -O3 -I${PREFIX}/include" \
+	--with-boost="${PREFIX}" \
+	--with-mpi="${PREFIX}" \
+	--with-sparsehash="${PREFIX}" \
+	--without-sqlite || cat config.log
+make AM_CXXFLAGS="-Wall" -j"${CPU_COUNT}"
 make install
 
 $RECIPE_DIR/create-wrapper.sh "$PREFIX/bin/abyss-pe" "$PREFIX/bin/abyss-pe.Makefile"

diff --git a/recipes/abyss/config.patch b/recipes/abyss/config.patch
diff --git a/recipes/abyss/meta.yaml b/recipes/abyss/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "abyss" %}
-{% set version = "2.3.9" %}
+{% set version = "2.3.10" %}
 
 package:
   name: {{ name|lower }}
@@ -12,20 +12,22 @@ build:
 
 source:
   url: https://github.com/bcgsc/abyss/releases/download/{{ version }}/abyss-{{ version }}.tar.gz
-  sha256: 55f0b27b67b4486dc6cbe132c0f4c228ee4f9e86c56292a7b50633df87e3212e
-  patches:
-    - config.patch
+  sha256: bbe42e00d1ebb53ec6afaad07779baaaee994aa5c65b9a38cf4ad2011bb93c65
 
 requirements:
   build:
     - {{ compiler('cxx') }}
     - make
+    - automake
+    - autoconf
+    - libtool
   host:
     - boost-cpp
     - sparsehash
     - openmpi
     - btllib
   run:
+    - boost-cpp
     - openmpi
     - make
     - util-linux  # [linux]
@@ -38,12 +40,13 @@ test:
     - abyss-pe help | grep -q "Assemble reads into contigs and scaffolds"
 
 about:
-  home: http://www.bcgsc.ca/platform/bioinfo/software/abyss
-  license: GPL-3.0-only
+  home: "https://www.bcgsc.ca/platform/bioinfo/software/abyss"
+  license: "GPL-3.0-only"
+  license_family: GPL3
   license_file: LICENSE
-  summary: Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler
-  dev_url: https://github.com/bcgsc/abyss
-  doc_url: https://github.com/bcgsc/abyss#readme
+  summary: "Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler."
+  dev_url: "https://github.com/bcgsc/abyss"
+  doc_url: "https://github.com/bcgsc/abyss/blob/v{{ version }}/README.md"
 
 extra:
   additional-platforms:
@@ -54,5 +57,6 @@ extra:
     extended-base: true
   identifiers:
     - biotools:abyss
+    - usegalaxy-eu:abyss-pe
     - doi:10.1101/gr.214346.116
     - doi:10.1101/gr.089532.108
diff --git a/recipes/afpdb/meta.yaml b/recipes/afpdb/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "afpdb" %}
-{% set version = "0.2.2" %}
+{% set version = "0.2.3" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: fbdc60785aba0177a3766f952df8bc848aa03adcc0693506cc9f1f3601449e98
+  sha256: aad8f90092630dce86254227bc94e4f42a28598a6ccf69f07d0e619bc88c0ae8
 
 build:
   number: 0

diff --git a/recipes/annembed/build.sh b/recipes/annembed/build.sh
@@ -5,4 +5,4 @@
 export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo"
 
 # build statically linked binary with Rust
-RUST_BACKTRACE=1 cargo install --features intel-mkl-static --verbose --path . --root $PREFIX
+RUST_BACKTRACE=1 cargo install --features intel-mkl-static,simdeez_f --verbose --path . --root $PREFIX
diff --git a/recipes/annembed/meta.yaml b/recipes/annembed/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.1.4" %}
+{% set version = "0.1.6" %}
 
 package:
   name: annembed
@@ -11,7 +11,7 @@ build:
   skip: True  # [osx]
 source:
   url: https://github.com/jianshu93/annembed/archive/v{{ version }}.tar.gz
-  sha256: 0f923798db3843aac0352eba5d2b169673ee087fce2cc37981bd19a1ecb878d0
+  sha256: f60dceb94df46ae2ccc7ed228988a67df254a28f02b9b545baf31ca6e85f7f8d
 
 requirements:
   build:
@@ -28,7 +28,7 @@ test:
 about:
   home: https://github.com/jianshu93/annembed
   license: MIT
-  summary: annembed is an ultra-fast and scalable non-linear dimension reduction algorithm (similar to UMAP or t-SNE) for large-scale biological data
+  summary: annembed is an ultra-fast and scalable non-linear dimension reduction/embedding algorithm (similar to UMAP or t-SNE) for large-scale biological data
 
 extra:
   maintainers:

diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "assembly_finder" %}
-{% set version = "0.7.7" %}
+{% set version = "0.8.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 0c6542253464b8ba406aeddc630f5625db74a5e1e07911534be3add0500a1f02
+  sha256: 8708d9185dccce21808777c79dad1c2b019ca1f416035c2e5e16b0c32928566e
 
 build:
   number: 0
@@ -20,17 +20,17 @@ build:
 
 requirements:
   host:
-    - python >=3.10
+    - python >=3.11
     - pip
+    - setuptools
   run:
-    - python >=3.10
-    - mamba >=1.5.8
+    - python >=3.11
     - snakemake-minimal >=8.0.0
     - snaketool-utils >=0.0.5
     - attrmap >=0.0.7
-    - pyyaml >=6.0
+    - pyyaml >=6.0.1
     - pandas >=2.2.1
-    - rich-click >=1.7.4
+    - rich-click >=1.8.3
 
 test:
   commands:

diff --git a/recipes/auspice/meta.yaml b/recipes/auspice/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.58.0" %}
+{% set version = "2.59.1" %}
 {% set name = "auspice" %}
 
 package:
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://registry.npmjs.org/{{ name }}/-/{{ name }}-{{ version }}.tgz
-  sha256: cb746010b28de5d0232258113820c551f6f4287e5b0ff67a1e5854adc381ac96
+  sha256: 828bc00e27ca3d403332686ab041dd3171c999a1a942b9fe89ba8256daedfecc
 
 build:
   number: 0
@@ -20,14 +20,14 @@ requirements:
     # vary across platforms.
     - "{{ compiler('c') }}"
     - "{{ compiler('cxx') }}"
-    - nodejs 16.*|18.*|20.*
+    - nodejs 16.*|18.*|20.*|22.*
     - python
     - pkg-config
     - yarn 1.*
   host:
     - icu
   run:
-    - nodejs 16.*|18.*|20.*
+    - nodejs 16.*|18.*|20.*|22.*
 
 test:
   commands:

diff --git a/recipes/bactopia-py/meta.yaml b/recipes/bactopia-py/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "bactopia-py" %}
-{% set version = "1.2.1" %}
+{% set version = "1.3.0" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/bactopia/bactopia-{{ version }}.tar.gz
-  sha256: bd375fcea02e5ea20c55f822a7173e70c89d30098585f4b3205bb85a94f821c1
+  sha256: ac777d8338823c5709d5d4ad3af719faf7084e4c1956fb108ae3d410ad6f74e8
 
 build:
   noarch: python
@@ -39,6 +39,7 @@ test:
     - bactopia-citations --help
     - bactopia-citations --version
     - bactopia-datasets --help
+    - bactopia-datasets --version
     - bactopia-download --help
     - bactopia-prepare --help
     - bactopia-search --help

diff --git a/recipes/biobb_amber/meta.yaml b/recipes/biobb_amber/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "biobb_amber" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 11fe9767c895c5de4a2e643f1c2de00f57bb03c8e0835415542c98aec2ca6040
+  sha256: 11ce0b1a7f7ec912136d31a46bffdc1c85b831686a51b8e9fe5e35cac611f09c
 
 build:
   number: 0
@@ -18,14 +18,14 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.8,<3.11
     - setuptools
-    - biobb_common ==4.2.0
-    - ambertools >=22.0
+    - biobb_common ==5.0.0
+    - ambertools ==22.5.0
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
-    - ambertools >=22.0
+    - python >=3.8,<3.11
+    - biobb_common ==5.0.0
+    - ambertools ==22.5.0
 
 test:
   imports: