Merge remote-tracking branch 'origin/devel' into HEAD for 4.10.0 release

.github/workflows/unit-tests.yml

@@ -25,7 +25,7 @@ jobs:
 
       - name: "Install dependencies"
         run: |
-          conda install conda-build pip
+          conda install conda==23.3 conda-build pip 
           python -m pip install --upgrade pip setuptools wheel
           pip install -r ./requirements.txt
           pip install -r ./test-requirements.txt

CHANGELOG.md

@@ -22,6 +22,30 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+#### Recipes
+
+## [4.10.0]
+
+### Added
+
+#### Recipes
+ - samtools 1.17
+ - bcftools 1.17
+ - htslib 1.17
+
+#### Features
+
+### Removed
+
+#### Recipes
+
+### Changed
+ - GH Actions: fix conda 23.3 to cope with API changes
+
+## [4.9.0]
+
+### Added
+
 #### Recipes
  - bambi 0.15.0
 

recipes/bcftools/1.17/build.sh

@@ -0,0 +1,11 @@
+#!/bin/sh
+
+set -ex
+
+n="$CPU_COUNT"
+
+./configure --prefix="$PREFIX" --with-htslib="$PREFIX" \
+  CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib"
+
+make -j "$n" 
+make install prefix="$PREFIX"

recipes/bcftools/1.17/meta.yaml

@@ -0,0 +1,36 @@
+{% set version = "1.17" %} # reset build to zero on changing
+{% set upstream_version = "1.17" %}
+{% set htslib_version = "1.17" %}  # Bump build version on change
+{% set sha256 = "01f75d8e701d85b2c759172412009cc04f29b61616ace2fa75116123de4596cc" %}
+
+package:
+  name: bcftools
+  version: "{{ version }}"
+
+about:
+  home: https://github.com/samtools/bcftools
+  license: MIT
+  summary: VCF commands and BCF calling.
+
+build:
+  number: 0
+
+source:
+  url: https://github.com/samtools/bcftools/releases/download/{{ upstream_version }}/bcftools-{{ upstream_version }}.tar.bz2
+  fn: bcftools-{{ upstream_version }}.tar.bz2
+  sha256: {{ sha256 }}
+
+requirements:
+  build:
+    - {{ compiler("c") }}
+    - make
+  host:
+    - libhts-dev =={{ htslib_version }}
+    - libz-dev
+  run:
+    - libhts =={{ htslib_version }}
+    - libz
+
+test:
+  commands:
+    - bcftools --help

recipes/htslib/1.17/build.sh

@@ -0,0 +1,23 @@
+#!/bin/sh
+
+set -ex
+
+n="$CPU_COUNT"
+
+pushd htslib
+
+autoreconf -i
+
+./configure \
+    --prefix="$PREFIX" \
+    --with-libdeflate \
+    --enable-libcurl \
+    --enable-s3 \
+    --enable-gcs \
+    --enable-plugins \
+    CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib"
+
+make -j "$n" AR="$AR"
+make install prefix="$PREFIX"
+popd
+

recipes/htslib/1.17/meta.yaml

@@ -0,0 +1,120 @@
+{% set version = "1.17" %} # reset build to zero on changing
+{% set htslib_rev = "6143086502567c5c4bb5cacb2951f664ba28ed6e" %}
+
+package:
+  name: htslib-pkg
+  version: "{{ version }}"
+
+about:
+  home: https://github.com/samtools/htslib
+  license: MIT
+  summary: C library for high-throughput sequencing data formats.
+
+build:
+  number: 0
+
+source:
+  - git_url: https://github.com/samtools/htslib.git
+    git_rev: {{ htslib_rev }}
+    folder: htslib
+
+requirements:
+  build:
+    - {{ compiler("c") }}
+    - autoconf
+    - automake
+    - make
+    - perl
+  host:
+    - libbz2-dev
+    - libcurl-dev
+    - libdeflate-dev
+    - liblzma-dev
+    - libssl-dev
+    - libz-dev
+  run:
+    - libbz2
+    - libcurl
+    - libdeflate
+    - liblzma
+    - libssl
+    - libz
+
+outputs:
+  - name: htslib
+    version: {{ version }}
+    requirements:
+      build:
+        - {{ compiler("c") }}
+        - autoconf
+        - automake
+        - make
+        - perl
+      host:
+        - libbz2-dev
+        - libcurl-dev
+        - libdeflate-dev
+        - liblzma-dev
+        - libssl-dev
+        - libz-dev
+      run:
+        - {{ pin_subpackage("libhts", exact=True) }}
+        - libbz2
+        - libcurl
+        - libdeflate
+        - liblzma
+        - libssl
+        - libz
+    files:
+      - bin/bgzip
+      - bin/htsfile
+      - bin/tabix
+      - share/man/man1/htsfile.1
+      - share/man/man1/tabix.1
+
+  - name: libhts
+    version: {{ version }}
+    requirements:
+      build:
+        - {{ compiler("c") }}
+        - autoconf
+        - automake
+        - make
+        - perl
+      host:
+        - libbz2-dev
+        - libcurl-dev
+        - libdeflate-dev
+        - liblzma-dev
+        - libssl-dev
+        - libz-dev
+      run:
+        - libbz2
+        - libcurl
+        - libdeflate
+        - liblzma
+        - libssl
+        - libz
+    files:
+      - libexec/htslib
+      - lib/libhts.so*
+    test:
+      commands:
+        - test -h ${PREFIX}/lib/libhts.so
+        - test -f ${PREFIX}/libexec/htslib/hfile_libcurl.so
+
+  - name: libhts-dev
+    version: {{ version }}
+    requirements:
+      run:
+        - {{ pin_subpackage("libhts", exact=True) }}
+    files:
+      - include/htslib
+      - lib/libhts.a
+      - share/man/man5/faidx.5
+      - share/man/man5/sam.5
+      - share/man/man5/vcf.5
+    test:
+      commands:
+        - test -f ${PREFIX}/lib/libhts.a
+        - test -f ${PREFIX}/include/htslib/sam.h

recipes/samtools/1.17/build.sh

@@ -0,0 +1,15 @@
+#!/bin/sh
+
+set -ex
+
+n="$CPU_COUNT"
+
+autoreconf -i
+
+./configure --prefix="$PREFIX" \
+            --with-htslib=system \
+            --without-curses \
+            CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib"
+
+make -j "$n" AR="$AR"
+make install prefix="$PREFIX"

recipes/samtools/1.17/meta.yaml

@@ -0,0 +1,65 @@
+{% set version = "1.17" %} # reset build to zero on changing
+{% set htslib_version = "1.17" %}
+
+package:
+  name: samtools-pkg
+  version: "{{ version }}"
+
+about:
+  home: https://github.com/samtools/samtools
+  license: MIT
+  summary: C library for high-throughput sequencing data formats.
+
+build:
+  number: 0
+
+source:
+  git_url: https://github.com/samtools/samtools.git
+  git_rev: 4959cc981ad9725d3c6007687ca372ffcdaa3c80
+
+requirements:
+  build:
+    - {{ compiler("c") }}
+    - autoconf
+    - automake
+    - make
+    - perl
+  host:
+    - libhts-dev =={{ htslib_version }}
+    - libz-dev
+  run:
+    - libhts =={{ htslib_version }}
+    - libz
+
+outputs:
+  - name: samtools
+    version: {{ version }}
+    requirements:
+      build:
+        - {{ compiler("c") }}
+        - autoconf
+        - automake
+        - make
+        - perl
+      host:
+        - libhts-dev =={{ htslib_version }}
+        - libz-dev
+      run:
+        - libhts =={{ htslib_version }}
+        - libz
+    files:
+      - bin/ace2sam
+      - bin/maq2sam-*
+      - bin/md5*
+      - bin/plot-ampliconstats
+      - bin/plot-bamstats
+      - bin/samtools
+      - bin/wgsim
+      - bin/*.pl
+      - bin/*.py
+      - share/man/man1/samtools*.1
+      - share/man/man1/wgsim.1
+    test:
+      commands:
+        - echo -e '@HD\tVN:1.0\tSO:unsorted' | samtools view
+        - samtools --help | grep Version:\ {{ version }}\ \(