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Update rna-seqc to 2.4.2 #51342

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merged 7 commits into from
Oct 11, 2024
+24 −17
Merged

Update rna-seqc to 2.4.2 #51342

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69aa6da
fix: Add python dependencies
lrvdijk Oct 11, 2024
b0d392c
enh: Add run_exports and add python import test
lrvdijk Oct 11, 2024
bf04c1e
fix: Place run_exports in correct location
lrvdijk Oct 11, 2024
cb0feb5
fix: Remove pip dependencies and reset build num
lrvdijk Oct 11, 2024
5317579
enh: Don't include python package installation
lrvdijk Oct 11, 2024
f017fab
fix: Fix license_file location
lrvdijk Oct 11, 2024
e9716b7
clean up recipe
mencian Oct 11, 2024
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9 changes: 5 additions & 4 deletions recipes/rna-seqc/build.sh
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Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
#!/bin/bash
set -eu -o pipefail

cd ./travis/build/broadinstitute/rnaseqc
export CFLAGS="${CFLAGS} -fcommon"
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
export CFLAGS="${CFLAGS} -O3 -fcommon"

cd rnaseqc
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pushd SeqLib/bwa
sed -i.bak '/^DFLAGS=/s/$/ $(LDFLAGS)/' Makefile
make CC="$CC" CFLAGS="$CFLAGS" LDFLAGS="$LDFLAGS"
Expand All @@ -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 \
Expand All @@ -28,5 +29,5 @@ make \
LIBRARY_PATHS="-L$PREFIX/lib -Wl,-rpath $PREFIX/lib"

mkdir -p $PREFIX/bin
chmod 0755 rnaseqc
cp rnaseqc $PREFIX/bin

32 changes: 19 additions & 13 deletions recipes/rna-seqc/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,16 +1,18 @@
{% set version = "2.3.5" %}
{% set sha256sum = "44e81f01f2b661a7621f34e3b645f5727bc7143841f1df053723e23ba298d2c6" %}
{% set version = "2.4.2" %}
{% 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: 6
number: 0
run_exports:
- {{ pin_subpackage("rna-seqc", max_pin="x") }}

requirements:
build:
Expand All @@ -25,19 +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: LICENSE # not distributed :-/
license: BSD 3-clause
license_file: rnaseqc/LICENSE
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