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recipe for pgrc #50973

Merged
merged 7 commits into from
Sep 27, 2024
Merged

recipe for pgrc #50973

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7d69ef4
recipe for pgrc
kowallus Sep 26, 2024
5e557e0
fixed build number and skipped osx
kowallus Sep 26, 2024
fe8a5a9
updates & simplifications
kowallus Sep 26, 2024
69cf7e3
Merge branch 'master' into add_pgrc20_recipe
kowallus Sep 26, 2024
7de3b62
remove ill-formed test
kowallus Sep 26, 2024
d8d1f0c
Merge branch 'add_pgrc20_recipe' of https://github.com/kowallus/bioco…
kowallus Sep 26, 2024
ba4a400
Merge branch 'master' into add_pgrc20_recipe
kowallus Sep 26, 2024
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14 changes: 14 additions & 0 deletions recipes/pgrc/build.sh
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Original file line number Diff line number Diff line change
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#! /bin/bash

mkdir -p $PREFIX/bin

mkdir build
cd build
Comment on lines +5 to +6
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⚠️ Potential issue

Improve error handling for directory change.

While the build directory creation is correct, it's important to handle potential failures when changing directories.

Apply this change to improve error handling:

 mkdir build
-cd build
+cd build || exit 1

This ensures the script exits if it fails to change to the build directory, preventing issues in subsequent steps.

📝 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
mkdir build
cd build
mkdir build
cd build || exit 1
🧰 Tools
🪛 Shellcheck

[warning] 6-6: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.

(SC2164)

export CPATH=${BUILD_PREFIX}/include
export CXXPATH=${BUILD_PREFIX}/include
export CXXFLAGS="$CFLAGS -I$BUILD_PREFIX/include"
export LDFLAGS="$LDFLAGS -L$BUILD_PREFIX/lib"
cmake ..
make -j ${CPU_COUNT} PgRC
Comment on lines +11 to +12
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🛠️ Refactor suggestion

Enhance build process with error handling and parallel jobs.

The build commands look good, but could benefit from improved error handling. The use of parallel jobs in the make command is excellent for performance.

Consider modifying the build commands as follows:

-cmake ..
-make -j ${CPU_COUNT} PgRC
+cmake .. || exit 1
+make -j${CPU_COUNT} PgRC || exit 1

These changes ensure that the script exits if either the cmake or make command fails, preventing issues with incomplete or failed builds. The space after -j has been removed as it's not necessary.

📝 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
cmake ..
make -j ${CPU_COUNT} PgRC
cmake .. || exit 1
make -j${CPU_COUNT} PgRC || exit 1


cp PgRC $PREFIX/bin
martin-g marked this conversation as resolved.
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38 changes: 38 additions & 0 deletions recipes/pgrc/meta.yaml
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{% set version = "2.0" %}
{% set sha256 = "b4f7c1020dcf83428ee04663e2d68e81b08ba5853c9edffb3d5d00ac0f361b92" %}

package:
name: pgrc
version: {{ version }}

build:
skip: True # [osx]
number: 0
run_exports:
- {{ pin_subpackage('pgrc', max_pin="x") }}

source:
url: https://github.com/kowallus/PgRC/archive/refs/tags/v{{ version }}.tar.gz
sha256: {{ sha256 }}

requirements:
build:
- {{ compiler('cxx') }}
- cmake >=3.5
- make

test:
commands:
- PgRC -v 2>&1 | grep -F {{ version }}
- PgRC -h

about:
home: https://github.com/kowallus/PgRC
license: GPL-3.0-or-later
license_file: LICENSE
license_family: GPL3
summary: A tool for compressing the DNA stream of FASTQ datasets

extra:
maintainers:
- kowallus
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