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Update rna-seqc to 2.4.2 #51342

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merged 7 commits into from
Oct 11, 2024
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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5 changes: 4 additions & 1 deletion recipes/rna-seqc/build.sh
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
#!/bin/bash
set -eu -o pipefail

cd ./travis/build/broadinstitute/rnaseqc
export CFLAGS="${CFLAGS} -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 @@ -30,3 +30,6 @@ make \
mkdir -p $PREFIX/bin
cp rnaseqc $PREFIX/bin

# Install python scripts
cd python
$PYTHON setup.py install
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🛠️ Refactor suggestion

Approved: Python script installation added

The addition of Python script installation aligns with the PR objectives. However, there's room for improvement in the installation method.

Consider using pip for installation instead of setup.py, as it's the recommended method for modern Python packaging:

 # Install python scripts
 cd python
-$PYTHON setup.py install
+$PYTHON -m pip install .

This change ensures that the package is installed with all its dependencies and metadata correctly handled by pip.

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
# Install python scripts
cd python
$PYTHON setup.py install
# Install python scripts
cd python
$PYTHON -m pip install .

21 changes: 16 additions & 5 deletions recipes/rna-seqc/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{% set version = "2.3.5" %}
{% set sha256sum = "44e81f01f2b661a7621f34e3b645f5727bc7143841f1df053723e23ba298d2c6" %}
{% set version = "2.4.2" %}
{% set sha256sum = "b214151408696430aead56921b255e2b09efe5f6087a68446deae399227a1303" %}

package:
name: rna-seqc
Expand All @@ -10,7 +10,9 @@ source:
sha256: '{{ sha256sum }}'

build:
number: 6
number: 1
run_exports:
- {{ pin_subpackage("rna-seqc", max_pin="x.x") }}

requirements:
build:
Expand All @@ -29,14 +31,23 @@ requirements:
- boost-cpp
- xz
- zlib
- numpy
- pandas
- matplotlib-base
- seaborn
- nbformat
- pip:
- agutil
test:
commands:
- rnaseqc --version
imports:
- rnaseqc

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
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