From 69aa6daf740e532c62fb1a636962ebeb42e7c9f8 Mon Sep 17 00:00:00 2001 From: Lucas van Dijk Date: Fri, 11 Oct 2024 11:51:55 -0500 Subject: [PATCH 1/7] fix: Add python dependencies --- recipes/rna-seqc/build.sh | 5 ++++- recipes/rna-seqc/meta.yaml | 17 ++++++++++++----- 2 files changed, 16 insertions(+), 6 deletions(-) diff --git a/recipes/rna-seqc/build.sh b/recipes/rna-seqc/build.sh index 7afd75451acd7..0b689901352b8 100644 --- a/recipes/rna-seqc/build.sh +++ b/recipes/rna-seqc/build.sh @@ -1,9 +1,9 @@ #!/bin/bash set -eu -o pipefail -cd ./travis/build/broadinstitute/rnaseqc export CFLAGS="${CFLAGS} -fcommon" +cd rnaseqc pushd SeqLib/bwa sed -i.bak '/^DFLAGS=/s/$/ $(LDFLAGS)/' Makefile make CC="$CC" CFLAGS="$CFLAGS" LDFLAGS="$LDFLAGS" @@ -30,3 +30,6 @@ make \ mkdir -p $PREFIX/bin cp rnaseqc $PREFIX/bin +# Install python scripts +cd python +$PYTHON setup.py install diff --git a/recipes/rna-seqc/meta.yaml b/recipes/rna-seqc/meta.yaml index f81f069b06e8e..1dd327ad49f68 100644 --- a/recipes/rna-seqc/meta.yaml +++ b/recipes/rna-seqc/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.3.5" %} -{% set sha256sum = "44e81f01f2b661a7621f34e3b645f5727bc7143841f1df053723e23ba298d2c6" %} +{% set version = "2.4.2" %} +{% set sha256sum = "b214151408696430aead56921b255e2b09efe5f6087a68446deae399227a1303" %} package: name: rna-seqc @@ -10,7 +10,7 @@ source: sha256: '{{ sha256sum }}' build: - number: 6 + number: 1 requirements: build: @@ -29,14 +29,21 @@ requirements: - boost-cpp - xz - zlib + - numpy + - pandas + - matplotlib-base + - seaborn + - nbformat + - pip: + - agutil test: commands: - rnaseqc --version about: - home: https://github.com/broadinstitute/rnaseqc + home: https://github.com/broadinstitute/rnaseqc license_url: https://raw.githubusercontent.com/broadinstitute/rnaseqc/master/LICENSE - # license_file: LICENSE # not distributed :-/ + license_file: LICENSE license: BSD 3-clause license_family: BSD summary: Fast, efficient RNA-Seq metrics for quality control and process optimization From b0d392ca57fbd8682b8ecef84c07f3abc5773819 Mon Sep 17 00:00:00 2001 From: Lucas van Dijk Date: Fri, 11 Oct 2024 11:59:16 -0500 Subject: [PATCH 2/7] enh: Add run_exports and add python import test --- recipes/rna-seqc/meta.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/recipes/rna-seqc/meta.yaml b/recipes/rna-seqc/meta.yaml index 1dd327ad49f68..4f925c169e019 100644 --- a/recipes/rna-seqc/meta.yaml +++ b/recipes/rna-seqc/meta.yaml @@ -17,6 +17,8 @@ requirements: - make - {{ compiler('cxx') }} - {{ compiler('c') }} + run_exports: + - {{ pin_subpackage("rna-seqc", max_pin="x.x") }} host: - curl - bzip2 @@ -39,6 +41,8 @@ requirements: test: commands: - rnaseqc --version + imports: + - rnaseqc about: home: https://github.com/broadinstitute/rnaseqc From bf04c1e2a938fdfa663148f568e62c314c2ebb94 Mon Sep 17 00:00:00 2001 From: Lucas van Dijk Date: Fri, 11 Oct 2024 12:05:43 -0500 Subject: [PATCH 3/7] fix: Place run_exports in correct location --- recipes/rna-seqc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rna-seqc/meta.yaml b/recipes/rna-seqc/meta.yaml index 4f925c169e019..eefeeb7f29561 100644 --- a/recipes/rna-seqc/meta.yaml +++ b/recipes/rna-seqc/meta.yaml @@ -11,14 +11,14 @@ source: build: number: 1 + run_exports: + - {{ pin_subpackage("rna-seqc", max_pin="x.x") }} requirements: build: - make - {{ compiler('cxx') }} - {{ compiler('c') }} - run_exports: - - {{ pin_subpackage("rna-seqc", max_pin="x.x") }} host: - curl - bzip2 From cb0feb56b66d774ab6462cf71b0d95e30caf08fc Mon Sep 17 00:00:00 2001 From: Lucas van Dijk Date: Fri, 11 Oct 2024 12:29:10 -0500 Subject: [PATCH 4/7] fix: Remove pip dependencies and reset build num --- recipes/rna-seqc/meta.yaml | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/recipes/rna-seqc/meta.yaml b/recipes/rna-seqc/meta.yaml index eefeeb7f29561..6443319a75953 100644 --- a/recipes/rna-seqc/meta.yaml +++ b/recipes/rna-seqc/meta.yaml @@ -2,17 +2,17 @@ {% set sha256sum = "b214151408696430aead56921b255e2b09efe5f6087a68446deae399227a1303" %} package: - name: rna-seqc - version: '{{ version }}' + name: "rna-seqc" + version: {{ version }} source: url: 'https://github.com/broadinstitute/rnaseqc/releases/download/v{{ version }}/rnaseqc.v{{ version }}.full_source.tar.gz' - sha256: '{{ sha256sum }}' + sha256: {{ sha256sum }} build: - number: 1 + number: 0 run_exports: - - {{ pin_subpackage("rna-seqc", max_pin="x.x") }} + - {{ pin_subpackage("rna-seqc", max_pin="x") }} requirements: build: @@ -36,8 +36,6 @@ requirements: - matplotlib-base - seaborn - nbformat - - pip: - - agutil test: commands: - rnaseqc --version From 53175792ab2fccc4f41c0db0a4c0a8c801b93a04 Mon Sep 17 00:00:00 2001 From: Lucas van Dijk Date: Fri, 11 Oct 2024 12:40:08 -0500 Subject: [PATCH 5/7] enh: Don't include python package installation Will create a separate recipe for that --- recipes/rna-seqc/build.sh | 4 ---- recipes/rna-seqc/meta.yaml | 7 ------- 2 files changed, 11 deletions(-) diff --git a/recipes/rna-seqc/build.sh b/recipes/rna-seqc/build.sh index 0b689901352b8..60bdc22b03705 100644 --- a/recipes/rna-seqc/build.sh +++ b/recipes/rna-seqc/build.sh @@ -29,7 +29,3 @@ make \ mkdir -p $PREFIX/bin cp rnaseqc $PREFIX/bin - -# Install python scripts -cd python -$PYTHON setup.py install diff --git a/recipes/rna-seqc/meta.yaml b/recipes/rna-seqc/meta.yaml index 6443319a75953..55e5e4370bda0 100644 --- a/recipes/rna-seqc/meta.yaml +++ b/recipes/rna-seqc/meta.yaml @@ -31,16 +31,9 @@ requirements: - boost-cpp - xz - zlib - - numpy - - pandas - - matplotlib-base - - seaborn - - nbformat test: commands: - rnaseqc --version - imports: - - rnaseqc about: home: https://github.com/broadinstitute/rnaseqc From f017fab2777ea94c25ef78c267602c2c20bb2bb7 Mon Sep 17 00:00:00 2001 From: Lucas van Dijk Date: Fri, 11 Oct 2024 13:13:00 -0500 Subject: [PATCH 6/7] fix: Fix license_file location --- recipes/rna-seqc/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/rna-seqc/meta.yaml b/recipes/rna-seqc/meta.yaml index 55e5e4370bda0..55f01b5da7007 100644 --- a/recipes/rna-seqc/meta.yaml +++ b/recipes/rna-seqc/meta.yaml @@ -38,7 +38,7 @@ test: about: home: https://github.com/broadinstitute/rnaseqc license_url: https://raw.githubusercontent.com/broadinstitute/rnaseqc/master/LICENSE - license_file: LICENSE + license_file: rnaseqc/LICENSE license: BSD 3-clause license_family: BSD summary: Fast, efficient RNA-Seq metrics for quality control and process optimization From e9716b795e5c0e62b99b1bd69bba14463b4b1bbc Mon Sep 17 00:00:00 2001 From: mencian Date: Fri, 11 Oct 2024 16:24:38 -0500 Subject: [PATCH 7/7] clean up recipe --- recipes/rna-seqc/build.sh | 6 ++++-- recipes/rna-seqc/meta.yaml | 16 ++++++++++------ 2 files changed, 14 insertions(+), 8 deletions(-) diff --git a/recipes/rna-seqc/build.sh b/recipes/rna-seqc/build.sh index 60bdc22b03705..926e8a8e5a0bd 100644 --- a/recipes/rna-seqc/build.sh +++ b/recipes/rna-seqc/build.sh @@ -1,7 +1,8 @@ #!/bin/bash set -eu -o pipefail -export CFLAGS="${CFLAGS} -fcommon" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 -fcommon" cd rnaseqc pushd SeqLib/bwa @@ -19,7 +20,7 @@ popd make \ CC="$CXX" \ - CPPFLAGS="-I$PREFIX/include -fcommon" \ + CPPFLAGS="${CPPFLAGS} -O3 -I$PREFIX/include -fcommon" \ SeqLib/lib/libseqlib.a make \ @@ -28,4 +29,5 @@ make \ LIBRARY_PATHS="-L$PREFIX/lib -Wl,-rpath $PREFIX/lib" mkdir -p $PREFIX/bin +chmod 0755 rnaseqc cp rnaseqc $PREFIX/bin diff --git a/recipes/rna-seqc/meta.yaml b/recipes/rna-seqc/meta.yaml index 55f01b5da7007..cc91a8ea6f068 100644 --- a/recipes/rna-seqc/meta.yaml +++ b/recipes/rna-seqc/meta.yaml @@ -27,19 +27,23 @@ requirements: - zlib run: - curl - - bzip2 - boost-cpp - - xz - - zlib + test: commands: - rnaseqc --version about: - home: https://github.com/broadinstitute/rnaseqc + home: "https://github.com/broadinstitute/rnaseqc" license_url: https://raw.githubusercontent.com/broadinstitute/rnaseqc/master/LICENSE license_file: rnaseqc/LICENSE - license: BSD 3-clause + license: "BSD-3-Clause" license_family: BSD - summary: Fast, efficient RNA-Seq metrics for quality control and process optimization + summary: "Fast, efficient RNA-Seq metrics for quality control and process optimization." + dev_url: "https://github.com/broadinstitute/rnaseqc" + doc_url: "https://github.com/getzlab/rnaseqc/blob/v{{ version }}/README.md" +extra: + identifiers: + - biotools:rna-seqc + - doi:10.1093/bioinformatics/btab135