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Update bustools to 0.44.1 #51514

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merged 3 commits into from
Oct 21, 2024
Merged

Update bustools to 0.44.1 #51514

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1eb1a3f
Update bustools to 0.44.1
BiocondaBot Oct 21, 2024
9e6ac5a
clean up recipe
mencian Oct 21, 2024
2bf19cc
revert to CPATH
mencian Oct 21, 2024
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23 changes: 17 additions & 6 deletions recipes/bustools/build.sh
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Original file line number Diff line number Diff line change
@@ -1,10 +1,21 @@
#!/bin/bash
set -euo pipefail

export CPATH=$PREFIX/include
export INCLUDE_PATH=$PREFIX/include
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⚠️ Potential issue

Use CPATH instead of INCLUDE_PATH for include directories

The environment variable CPATH is recognized by compilers like GCC and Clang to specify additional include directories. INCLUDE_PATH is not commonly used by compilers and may not have the intended effect. To ensure that the compiler includes the necessary headers from $PREFIX/include, it's recommended to use CPATH.

Apply this diff to fix the issue:

-export INCLUDE_PATH=$PREFIX/include
+export CPATH=$PREFIX/include
📝 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
export INCLUDE_PATH=$PREFIX/include
export CPATH=$PREFIX/include

export LIBRARY_PATH=$PREFIX/lib
export LDFLAGS="${LDFLAGS} -L$PREFIX/lib"
export CXXFLAGS="${CXXFLAGS} -std=c++14 -O3 -I${PREFIX}/include"

mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX:PATH=$PREFIX ..
make
make install
if [[ `uname` == "Darwin" ]]; then
export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
else
export CONFIG_ARGS=""
fi

cmake -S. -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
-DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \
-DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DCMAKE_C_COMPILER="${CC}" \
-DCMAKE_C_FLAGS="${CFLAGS} -O3" \
"${CONFIG_ARGS}"

cmake --build build --target install -v
13 changes: 9 additions & 4 deletions recipes/bustools/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
{% set version = "0.44.0" %}
{% set version = "0.44.1" %}

package:
name: bustools
version: {{ version }}

source:
url: https://github.com/BUStools/bustools/archive/v{{ version }}.tar.gz
sha256: e9a12be416d5d3940dd0ec3bfb0be3a481f2eea7d4411df1ab24c814332d99b8
sha256: 829d7ca129b4c4911cae35bc2b87cac5d3a7845387b9a6487765aec84108d732

build:
number: 0
Expand All @@ -27,14 +27,19 @@ test:
- bustools sort

about:
home: https://github.com/BUStools/bustools
license: BSD-2-Clause "Simplified" License
home: "https://github.com/BUStools/bustools"
license: 'BSD-2-Clause "Simplified" License'
license_family: BSD
license_file: LICENSE
summary: |
bustools is a program for manipulating BUS files for single cell RNA-Seq datasets.
dev_url: "https://github.com/BUStools/bustools"
doc_url: "https://bustools.github.io/manual"

extra:
additional-platforms:
- linux-aarch64
- osx-arm64
identifiers:
- biotools:BUStools
- doi:10.1038/s41587-021-00870-2
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