Merge branch 'master' into bump/phables

recipes/bioconda-utils/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "bioconda-utils" %}
-{% set version = "3.3.1" %}
-{% set sha256 = "db6b99456a334b958ba61fcfc6e717e5f22848342f99fecb1f6f2b0113165054" %}
+{% set version = "3.3.2" %}
+{% set sha256 = "6c6dcac689a2fb0f8142546aa9021bfd620fe484e724e4844a2d2e55c337747c" %}
 
 package:
   name: {{ name }}
@@ -21,7 +21,7 @@ build:
 
 requirements:
   host:
-    - python
+    - python <3.12
     - pip
   run:
     - conda-forge-pinning 2024.06.01.05.54.15

recipes/catfasta2phyml/meta.yaml

@@ -1,14 +1,16 @@
 package:
   name: catfasta2phyml
-  version: "1.2.0"
+  version: "1.2.1"
 
 source:
-  url: https://github.com/nylander/catfasta2phyml/archive/refs/tags/v.1.2.0.tar.gz
-  sha256: f4ea5aef5aa21d15d84436262f06b79a004b7017ab7a433019fe903aec995fdb
+  url: https://github.com/nylander/catfasta2phyml/archive/refs/tags/v1.2.1.tar.gz
+  sha256: 2647985192b05df49e10bfce64d6843fe7916b0395199dfd2ac4f80910c5a91f
 
 build:
   number: 0
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage('catfasta2phyml', max_pin="x") }}
 
 requirements:
   run:

recipes/cpstools/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "cpstools" %}
-{% set version = "1.0.13" %}
-{% set sha256 = "767f5739416f290726ed459bf82969b453ffd2c04aa9171e5dc7c842a8d6b81e" %}
+{% set version = "2.0.0" %}
+{% set sha256 = "1c2c729d4979402d9f7835dea70e47c77d2e2ef6b1e822cfd1e6e008f3b98ba1" %}
 
 package:
   name: {{ name|lower }}
@@ -21,13 +21,14 @@ build:
 
 requirements:
   host:
-    - python >=3.10
+    - python >=3.9
     - poetry-core
     - pip
   run:
-    - python >=3.10.0
+    - python >=3.9
     - biopython >=1.84.0
     - numpy >=1.26.4
+    - tqdm >=4.66.5
 
 test:
   imports:

recipes/dbghaplo/build.sh

@@ -0,0 +1,10 @@
+#!/bin/bash -euo
+
+# Add workaround for SSH-based Git connections from Rust/cargo.  See https://github.com/rust-lang/cargo/issues/2078 for details.
+# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct.
+export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo"
+
+# build statically linked binary with Rust
+cargo-bundle-licenses --format yaml --output THIRDPARTY.yml
+RUST_BACKTRACE=1 cargo install --verbose --locked --no-track --root $PREFIX --path .
+cp scripts/* $PREFIX/bin

recipes/dbghaplo/meta.yaml

@@ -0,0 +1,47 @@
+{% set version="0.0.2" %}
+
+package:
+  name: dbghaplo
+  version: {{ version }}
+
+source:
+  url: https://github.com/bluenote-1577/dbghaplo/archive/v{{ version }}.tar.gz
+  sha256: e7e2741afb0c7f12718ec969815d3c8f18ce7ba66517e21c6fcfb3fe4262780b
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('dbghaplo', max_pin="x.x") }}
+
+requirements:
+  build:
+    - {{ compiler("cxx") }}
+    - {{ compiler('rust') }} 
+    - cargo-bundle-licenses
+    - make
+    - cmake >=3.12
+  run:
+    - python 
+    - samtools
+    - minimap2
+    - lofreq >=2.1.5
+    - tabix
+    - pysam >=0.16
+
+test:
+  commands:
+    - dbghaplo -h
+    - run_dbghaplo_pipeline -h
+    - haplotag_bam -h
+
+about:
+  home: https://github.com/bluenote-1577/dbghaplo
+  license: MIT
+  license_file:
+    - LICENSE
+    - THIRDPARTY.yml 
+  summary: Haplotyping small sequences from heterogeneous long-read sequencing samples with a SNP-encoded positional de Bruijn Graph.
+
+extra:
+  recipe-maintainers:
+    - bluenote-1577

recipes/hsdecipher/meta.yaml

@@ -1,16 +1,16 @@
 {% set name = "HSDecipher" %}
-{% set version = "1.0.0" %}
+{% set version = "1.1.1" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://github.com/zx0223winner/{{name|lower}}_conda/archive/refs/tags/v{{version}}.tar.gz
-  sha256: 54ab84f8584c69a50db4678b49279b0a0b4b05cf0028eec9c2f2ea2205917b76
+  sha256: 7ac882c835b53a78e4dfe5120037a8237f5e79a5ab94d7d0edd893d5851007ba
 
 build:
-  number: 1
+  number: 0
   noarch: python
   script: bash conda_build_package.sh
   run_exports:

recipes/pgrc/build.sh

@@ -1,14 +1,23 @@
-#! /bin/bash
+#!/bin/bash
 
 mkdir -p $PREFIX/bin
 
-mkdir build
-cd build
-export CPATH=${BUILD_PREFIX}/include
-export CXXPATH=${BUILD_PREFIX}/include
-export CXXFLAGS="$CFLAGS -I$BUILD_PREFIX/include"
-export LDFLAGS="$LDFLAGS -L$BUILD_PREFIX/lib"
-cmake ..
-make -j ${CPU_COUNT} PgRC
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 
-cp PgRC $PREFIX/bin
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi	
+
+cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	-DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+	"${CONFIG_ARGS}"
+cmake --build build --target PgRC -j "${CPU_COUNT}" -v
+
+chmod 0755 build/PgRC
+cp -rf build/PgRC $PREFIX/bin

recipes/pgrc/meta.yaml

@@ -6,8 +6,8 @@ package:
   version: {{ version }}
 
 build:
+  number: 1
   skip: True  # [osx]
-  number: 0
   run_exports:
     - {{ pin_subpackage('pgrc', max_pin="x") }}
 
@@ -20,18 +20,29 @@ requirements:
     - {{ compiler('cxx') }}
     - cmake >=3.5
     - make
+  host:
+    - llvm-openmp  # [osx]
+    - libgomp  # [linux]
+  run:
+    - llvm-openmp  # [osx]
+    - libgomp  # [linux]
 
 test:
   commands:
     - PgRC -v 2>&1 | grep -F {{ version }}
 
 about:
   home: https://github.com/kowallus/PgRC
-  license: GPL-3.0-or-later
+  license: "GPL-3.0-or-later"
   license_file: LICENSE
   license_family: GPL3
-  summary: A tool for compressing the DNA stream of FASTQ datasets
+  summary: "A tool for compressing the DNA stream of FASTQ datasets."
+  dev_url: https://github.com/kowallus/PgRC
 
 extra:
-  maintainers:
+  additional-platforms:
+    - linux-aarch64
+  recipe-maintainers:
     - kowallus
+  identifiers:
+    - doi:10.1093/bioinformatics/btz919

recipes/pybiolib/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "pybiolib" %}
-{% set version = "1.2.181" %}
+{% set version = "1.2.185" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz
-  sha256: 6025ec0898d20ea83593144619b1c94b5f99b46955205a74537b97270924ce7f
+  sha256: 9525f0548dd11df88b33845ecf51d17ee9c2c5675a0723ebf5c25c586c58e598
 
 build:
   number: 0

recipes/pypints/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "pyPINTS" %}
-{% set version = "1.1.10" %}
+{% set version = "1.1.13" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 91e4e6e8a308ad4e4e829068b96282385a0285512a2351cedd9793c50e8a7f63
+  url: "https://files.pythonhosted.org/packages/df/b4/0b6ded0841b01d72c2beb676b71ea94800896ec69c937f09acee24964597/pypints-1.1.13.tar.gz"
+  sha256: 808fca4e7fa6ff06dffebc49c36680c872044b4babdd9e42f012fa2ff140aa3e
 
 build:
   number: 0

recipes/pytximport/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "pytximport" %}
-{% set version = "0.8.0" %}
+{% set version = "0.9.0" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pytximport-{{ version }}.tar.gz
-  sha256: 18bdf4fbcd78092bba18f6941f5640a937b4f0230c30c2e8fca38ce207b3840b
+  sha256: f311705a71faa095d7e65de63235df55c805fbab4fbea10010fdae11014b3c95
 
 build:
   noarch: python

recipes/seqfu/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "seqfu" %}
-{% set version = "1.22.0" %}
-{% set sha256 = "e1b9032caab8e2effcc5a075b372c2fae636494b06e3bf2f30086c8d39fb5281" %}
+{% set version = "1.22.2" %}
+{% set sha256 = "0b66405ca98a80be614874fd1c1f651ecb410d953ac5070a0e93c77d2dbe1919" %}
 
 package:
   name: {{ name }}

recipes/sizemeup/meta.yaml

@@ -1,48 +1,49 @@
-{% set name = "sizemeup" %}
-{% set version = "1.0.2" %}
-
-package:
-  name: {{ name|lower }}
-  version: {{ version }}
-
-source:
-  url: https://github.com/rpetit3/sizemeup/archive/v{{ version }}.tar.gz
-  sha256: 0290d945909e20ccd417e4a874c22e14f5904695586974a98424dd9890bc9550
-
-build:
-  number: 0
-  noarch: generic
-  run_exports:
-    - {{ pin_subpackage(name, max_pin='x.x') }}
-
-requirements:
-  host:
-    - python >=3.7
-    - poetry
-    - pip
-  run:
-    - python >=3.7
-    - requests
-    - rich-click >=1.6.0
-
-test:
-  imports:
-    - sizemeup
-  commands:
-    - pip check
-    - sizemeup --version
-    - sizemeup --help
-    - sizemeup --species "Staphylococcus aureus"
-    - sizemeup-build --help
-  requires:
-    - pip
-
-about:
-  home: https://github.com/rpetit3/sizemeup
-  summary: A simple tool to determine the genome size of an organism
-  license: MIT
-  license_file: LICENSE
-
-extra:
-  recipe-maintainers:
-    - rpetit3
+{% set name = "sizemeup" %}
+{% set version = "1.1.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/rpetit3/sizemeup/archive/v{{ version }}.tar.gz
+  sha256: 3941e0b6affa2ba69c6ee01875d38ed8a94b864fbf51c4971a811d5483a61b8c
+
+build:
+  number: 0
+  noarch: generic
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x.x') }}
+
+requirements:
+  host:
+    - python >=3.7
+    - poetry
+    - pip
+  run:
+    - python >=3.7
+    - requests
+    - rich-click >=1.6.0
+
+test:
+  imports:
+    - sizemeup
+  commands:
+    - pip check
+    - sizemeup --version
+    - sizemeup --help
+    - sizemeup --query "Staphylococcus aureus"
+    - sizemeup -q 1280
+    - sizemeup-build --help
+  requires:
+    - pip
+
+about:
+  home: https://github.com/rpetit3/sizemeup
+  summary: A simple tool to determine the genome size of an organism
+  license: MIT
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - rpetit3

recipes/slow5tools/meta.yaml

@@ -1,16 +1,16 @@
 {% set name = "slow5tools" %}
-{% set version = "1.2.0" %}
+{% set version = "1.3.0" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/hasindu2008/slow5tools/releases/download/v{{ version }}/slow5tools-v{{ version }}-release.tar.gz
-  sha256: ce9d198f8368e90f440fce974e798b7f521b0fe4f859caf9a452bba1ca5af2d4
+  sha256: f7221285e0090a5ca05a75f5e70c51d093138b2c8ad658b2756c3c6e51097d5d
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('slow5tools', max_pin="x") }}