redundans: add linux-aarch64 build #52233
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces modifications to the Possibly related PRs
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🧹 Outside diff range and nitpick comments (4)
recipes/redundans/build.sh (4)
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6-11: Consider adding error checking for chmod operationWhile the directory creation and structure look good, the chmod operation could benefit from error handling to ensure the script fails appropriately if permissions can't be set.
-chmod u+x redundans.py #To avoid permission issues +if ! chmod u+x redundans.py; then + echo "Error: Failed to set execute permission on redundans.py" + exit 1 +fi
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14-14: Clean up the sed backup fileThe sed command creates a .bak file that should be removed to keep the installation directory clean.
-sed -i.bak 's|bin/SSPACE/SSPACE_Standard_v3.0.pl|SSPACE/SSPACE_Standard_v3.0.pl|g' redundans.py +sed -i.bak 's|bin/SSPACE/SSPACE_Standard_v3.0.pl|SSPACE/SSPACE_Standard_v3.0.pl|g' redundans.py && rm redundans.py.bak
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17-19: Optimize file copying operationsThe current implementation has several inefficiencies:
- Multiple separate cp commands increase script complexity
- Test directory is unnecessarily duplicated in both locations
- No error checking for copy operations
Consider consolidating the copy operations and adding error checking:
-cp redundans.py $INSTALL_FOLDER/ && cp redundans.py $BIN_FOLDER && cp README.md $INSTALL_FOLDER/ -cp -r test/ $INSTALL_FOLDER/ && cp -r test/ $BIN_FOLDER && cp -r docs/ $INSTALL_FOLDER/ && cp LICENSE $INSTALL_FOLDER/ +# Create a function for safer copy operations +copy_with_check() { + if ! cp "$@"; then + echo "Error: Failed to copy $@" + exit 1 + fi +} + +# Copy files more efficiently +copy_with_check redundans.py $INSTALL_FOLDER/ +copy_with_check redundans.py $BIN_FOLDER/ +copy_with_check README.md LICENSE $INSTALL_FOLDER/ +copy_with_check -r test/ docs/ $INSTALL_FOLDER/ +ln -s $INSTALL_FOLDER/test $BIN_FOLDER/test # Symlink instead of duplicate
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25-29: Security and reliability concerns in binary handlingThere are several issues to address:
- The permission setting of 777 is too permissive
- No verification of successful compilation
- The working directory changes could be safer
Consider these improvements:
-cd $BIN_FOLDER/last/ && make clean && make -j ${CPU_COUNT} && cd .. -cp -t $BIN_FOLDER $BIN_FOLDER/last/bin/* -chmod -R 777 $BIN_FOLDER/test/ && cd .. +# Save current directory +CURRENT_DIR=$(pwd) + +# Compile with error checking +cd $BIN_FOLDER/last/ || exit 1 +make clean || exit 1 +make -j ${CPU_COUNT} || exit 1 +cd .. + +# Copy binaries with verification +if ! cp -t $BIN_FOLDER $BIN_FOLDER/last/bin/*; then + echo "Error: Failed to copy last binaries" + exit 1 +fi + +# Set more restrictive permissions +chmod -R u=rwX,g=rX,o=rX $BIN_FOLDER/test/ + +# Return to original directory +cd "$CURRENT_DIR" || exit 1
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recipes/redundans/build.sh(1 hunks)recipes/redundans/meta.yaml(2 hunks)
🔇 Additional comments (4)
recipes/redundans/meta.yaml (2)
14-14: LGTM: Build number increment is appropriate
The build number increment is correct for adding new platform support.
63-64: Verify dependency compatibility for linux-aarch64
The addition of linux-aarch64 platform support looks good. However, please verify that all dependencies (especially binary ones like minimap2, miniasm, bwa, etc.) are available and tested for the aarch64 architecture in the bioconda channel.
recipes/redundans/build.sh (2)
3-3: Good addition of error handling!
The addition of set -xe improves build reliability by failing fast on errors and providing better debugging information through command echoing.
Line range hint 1-29: Verify aarch64 compatibility of all binary components
Since this PR adds linux-aarch64 support, please ensure:
- All compilation steps support aarch64 architecture
- Any pre-compiled binaries (like k8-Linux, platanus, GapCloser) have aarch64 versions available
- The make process for 'last' is tested on aarch64
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Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
Trying to solve: ``` ─ python >=3.10,<3.11.0a0 is not installable because there are no viable options 11:18:43 BIOCONDA INFO (OUT) ├─ python [3.10.0|3.10.1|...|3.10.9] would require 11:18:43 BIOCONDA INFO (OUT) │ └─ python_abi 3.10.* *_cp310, which conflicts with any installable versions previously reported; 11:18:43 BIOCONDA INFO (OUT) └─ python 3.10.15 would require 11:18:43 BIOCONDA INFO (OUT) └─ libzlib >=1.3.1,<2.0a0 , which conflicts with any installable versions previously reported ```
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