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Rebuild bam-readcount recipe #52212

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Rebuild bam-readcount recipe #52212

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10c1b48
Rebuild bam-readcount recipe
mencian Nov 20, 2024
f88c7ce
Update meta.yaml
mencian Nov 20, 2024
81676be
Update meta.yaml
mencian Nov 20, 2024
70c23be
Update build.sh
mencian Nov 20, 2024
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22 changes: 9 additions & 13 deletions recipes/bam-readcount/build.sh
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
#!/bin/bash -ex

wget https://github.com/boostorg/boost/releases/download/boost-1.85.0/boost-1.85.0-cmake.tar.gz
wget https://github.com/boostorg/boost/releases/download/boost-1.86.0/boost-1.86.0-cmake.tar.gz

mv boost-1.85.0-cmake.tar.gz vendor/boost-1.55-bamrc.tar.gz
mv boost-1.86.0-cmake.tar.gz vendor/boost-1.55-bamrc.tar.gz

mkdir -p "${PREFIX}/bin"
ln -sf $(which libtool) "${PREFIX}/bin/libtool"
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⚠️ Potential issue

Fix command substitution quoting

The command substitution should be quoted to prevent word splitting issues if the path contains spaces.

Apply this fix:

-ln -sf $(which libtool) "${PREFIX}/bin/libtool"
+ln -sf "$(which libtool)" "${PREFIX}/bin/libtool"
📝 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
ln -sf $(which libtool) "${PREFIX}/bin/libtool"
ln -sf "$(which libtool)" "${PREFIX}/bin/libtool"
🧰 Tools
🪛 Shellcheck

[warning] 7-7: Quote this to prevent word splitting.

(SC2046)


# Needed for building utils dependency
export INCLUDES="-I{PREFIX}/include"
Expand All @@ -14,26 +14,22 @@ export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"

if [[ `uname` == Darwin ]]; then
export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib"
export CFLAGS="${CFLAGS} -Wno-unguarded-availability -Wdeprecated-non-prototype"
export CFLAGS="${CFLAGS} -Wno-unguarded-availability -Wno-deprecated-non-prototype"
export CMAKE_EXTRA="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
else
export CMAKE_EXTRA=""
fi

mkdir -p build
pushd build
cmake -S .. -B . -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_CXX_COMPILER="${CXX}" \
-DCMAKE_C_COMPILER="${CC}" \
-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
-DCMAKE_C_FLAGS="${CFLAGS}" \
-Wno-dev -Wno-deprecated --no-warn-unused-cli \
${CMAKE_EXTRA}
"${CMAKE_EXTRA}"

make clean
make CXX="${CXX} ${LDFLAGS}" CC="${CC}" CXXFLAGS="${CXXFLAGS}" CFLAGS="${CFLAGS}"
cmake --build build -j "${CPU_COUNT}" -v

chmod 755 bin/bam-readcount
cp -f bin/bam-readcount "${PREFIX}/bin"
popd
install -d "$PREFIX/bin"
install -v -m 0755 build/bin/bam-readcount "$PREFIX/bin"
15 changes: 11 additions & 4 deletions recipes/bam-readcount/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,11 @@ package:
version: {{ version }}

source:
url: https://github.com/genome/{{ name }}/archive/v{{ version }}.tar.gz
sha256: 8ebf84d9efee0f2d3b43f0452dbf16b27337c960e25128f6a7173119e62588b8
git_url: https://github.com/genome/bam-readcount.git
git_rev: v{{ version }}
Comment on lines +9 to +10
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⚠️ Potential issue

Consider using tarball URL instead of git source for better reproducibility

Using VCS URLs in conda recipes can lead to reproducibility issues. It's recommended to use a tarball URL with a sha256 hash instead.

Apply this diff to improve build reproducibility:

-  git_url: https://github.com/genome/bam-readcount.git
-  git_rev: v{{ version }}
+  url: https://github.com/genome/bam-readcount/archive/v{{ version }}.tar.gz
+  sha256: # Add the appropriate sha256 hash here

Committable suggestion skipped: line range outside the PR's diff.


build:
number: 2
number: 3
run_exports:
- {{ pin_subpackage('bam-readcount', max_pin="x") }}

Expand All @@ -20,6 +20,9 @@ requirements:
- cmake
- {{ compiler('cxx') }}
- {{ compiler('c') }}
- autoconf
- automake
- libtool
host:
- zlib
- pthread-stubs
Expand All @@ -39,11 +42,15 @@ about:
license_file: LICENSE
summary: "bam-readcount generates metrics at single nucleotide positions."
dev_url: "https://github.com/genome/bam-readcount"
doc_url: "https://github.com/genome/bam-readcount/blob/master/README.md"
doc_url: "https://github.com/genome/bam-readcount/blob/v{{ version }}/README.md"

extra:
additional-platforms:
- linux-aarch64
- osx-arm64
identifiers:
- doi:10.21105/joss.03722
- biotools:bam-readcount
skip-lints:
- uses_vcs_url
- missing_hash
Comment on lines +54 to +56
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🛠️ Refactor suggestion

Remove skip-lints by fixing the source configuration

These lint skips are only necessary because of the git source usage. They can be removed by switching back to a tarball URL with sha256 hash as suggested earlier.

-  skip-lints:
-    - uses_vcs_url
-    - missing_hash
📝 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
skip-lints:
- uses_vcs_url
- missing_hash

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