Merge pull request #354 from wtsi-npg/devel

Pull from devel to master to create release 4.6.0

.github/workflows/unit-tests.yml

@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 jobs:
   build:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
 
     defaults:
       run:

CHANGELOG.md

@@ -18,6 +18,35 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+## [4.6.0]
+
+### Added
+
+#### Recipes
+ - samtools 1.16.1
+ - bcftools 1.16
+ - htslib 1.16
+
+#### Features
+
+### Removed
+
+#### Recipes
+ - irods 4.2.10
+
+### Changed
+ - Github Actions: Move from ubuntu-18.04 to ubuntu-latest
+
+#### Recipes
+ - Build config with compiler version and cflags and increment build number:
+   - avrocpp 1.8.2, 1.9.0
+   - boost 1.73.0
+ - Remove irods 4.2.10 from build config:
+   - baton 3.1.0, 3.2.0, 3.3.0, 4.0.0
+   - htslib-plugins 201712
+ - Update release url:
+   - libarchive
+
 ## [4.5.0]
 
 ### Added

recipes/avrocpp/1.8.2/conda_build_config.yaml

@@ -0,0 +1,16 @@
+c_compiler_version:
+  - 9.3
+
+cxx_compiler_version:
+  - 9.3
+
+CFLAGS: >-
+  -O2
+  -fPIC
+  -ffunction-sections
+  -fno-plt
+  -fstack-protector-strong
+  -ftree-vectorize
+  -march=x86-64
+  -mtune=generic
+  -pipe

recipes/avrocpp/1.8.2/meta.yaml

@@ -12,7 +12,7 @@ source:
   sha1: {{ hash }}
 
 build:
-  number: 4
+  number: 5
 
 requirements:
   build:

recipes/avrocpp/1.9.0/conda_build_config.yaml

@@ -0,0 +1,16 @@
+c_compiler_version:
+  - 9.3
+
+cxx_compiler_version:
+  - 9.3
+
+CFLAGS: >-
+  -O2
+  -fPIC
+  -ffunction-sections
+  -fno-plt
+  -fstack-protector-strong
+  -ftree-vectorize
+  -march=x86-64
+  -mtune=generic
+  -pipe

recipes/avrocpp/1.9.0/meta.yaml

@@ -12,7 +12,7 @@ source:
   sha1: {{ hash }}
 
 build:
-  number: 4
+  number: 5
 
 requirements:
   build:

recipes/baton/3.1.0/conda_build_config.yaml

@@ -1,4 +1,3 @@
 
 irods:
   - 4.2.7
-  - 4.2.10

recipes/baton/3.2.0/conda_build_config.yaml

@@ -1,5 +1,4 @@
 
 irods:
   - 4.2.7
-  - 4.2.10
   - 4.2.11

recipes/baton/3.3.0/conda_build_config.yaml

@@ -1,5 +1,4 @@
 
 irods:
   - 4.2.7
-  - 4.2.10
   - 4.2.11

recipes/baton/4.0.0/conda_build_config.yaml

@@ -1,5 +1,4 @@
 
 irods:
   - 4.2.7
-  - 4.2.10
   - 4.2.11

recipes/bcftools/1.16/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/1.16/meta.yaml

@@ -0,0 +1,36 @@
+{% set version = "1.16" %} # reset build to zero on changing
+{% set upstream_version = "1.16" %}
+{% set htslib_version = "1.16" %}  # Bump build version on change
+{% set sha256 = "90bf647c9ad79e10a243b8058c873de057fd7012e250d5ae6574839787a2ecd6" %}
+
+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/boost/1.73.0/conda_build_config.yaml

@@ -1,3 +1,9 @@
+c_compiler_version:
+  - 9.3
+
+cxx_compiler_version:
+  - 9.3
+
 CFLAGS: >-
   -O2
   -fPIC

recipes/boost/1.73.0/meta.yaml

@@ -12,7 +12,7 @@ about:
   summary: "Free peer-reviewed portable C++ source libraries."
 
 build:
-  number: 2
+  number: 3
 
 source:
   url: https://boostorg.jfrog.io/artifactory/main/release/{{ version }}/source/boost_{{ alt_version }}.tar.bz2

recipes/htslib-plugins/201712/conda_build_config.yaml

@@ -1,5 +1,4 @@
 
 irods:
   - 4.2.7
-  - 4.2.10
   - 4.2.11

recipes/htslib/1.16/build.sh

@@ -0,0 +1,24 @@
+#!/bin/sh
+
+set -ex
+
+n="$CPU_COUNT"
+
+pushd htslib
+
+autoheader
+autoconf
+
+./configure \
+    --prefix="$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/1.16/meta.yaml

@@ -0,0 +1,120 @@
+{% set version = "1.16" %} # reset build to zero on changing
+{% set htslib_rev = "4e61c128238f3e7cbb3b1f4e9c0fdb4880aa9a10" %}
+
+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