Racon: add arm64 build #52209
Racon: add arm64 build #52209
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📝 WalkthroughWalkthroughThe pull request introduces several modifications to the Racon package, primarily focusing on enhancing support for the Possibly related PRs
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (4)
recipes/racon/build.sh (2)
25-29: Consider conditional verbose output.The build configuration is well-structured using modern CMake practices. However, the verbose flag (-v) might generate excessive output in CI logs.
Consider making verbose output conditional:
-cmake --build build --target install -j "${CPU_COUNT}" -v +cmake --build build --target install -j "${CPU_COUNT}" ${VERBOSE_BUILD:+-v}
31-32: Add error handling for wrapper operations.While the operations are correct, consider adding error checking to handle cases where the wrapper build might fail.
Consider this safer approach:
-chmod +w build/bin/racon_wrapper -cp -f build/bin/racon_wrapper ${PREFIX}/bin +if [ -f build/bin/racon_wrapper ]; then + chmod +w build/bin/racon_wrapper + cp -f build/bin/racon_wrapper ${PREFIX}/bin +else + echo "Error: racon_wrapper not found in build/bin" >&2 + exit 1 +firecipes/racon/meta.yaml (2)
37-41: Consider improving documentation URLWhile the added metadata fields are good, pointing
doc_urlto the README.md file might not be the best practice. Consider creating more comprehensive documentation (e.g., ReadTheDocs, Wiki) for better user experience.
Based on the analysis of similar arm64-compatible packages in the output, I can generate the final response:
Add zlib to run requirements and include OpenMP dependencies
Please update the dependencies section to include:
- Add
zlibtorunrequirements since it's needed at runtime (seen in multiple similar packages)- Add OpenMP dependencies for proper arm64 support:
host: - llvm-openmp # [osx] - libgomp # [linux] run: - llvm-openmp # [osx] - libgomp # [linux]🔗 Analysis chain
Line range hint
18-28: Verify dependencies for arm64 buildPlease ensure all necessary dependencies are included for arm64 support:
- Verify if zlib is needed in
runrequirements- Check if there are any architecture-specific dependencies needed for arm64
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for architecture-specific dependencies in similar bioconda packages # Look for patterns in other arm64-compatible packages rg -l "osx-arm64" | xargs cat | rg "requirements:" -A 10Length of output: 49484
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📒 Files selected for processing (3)
recipes/racon/build.sh(1 hunks)recipes/racon/meta.yaml(2 hunks)recipes/racon/racon_wrapper.patch(0 hunks)
💤 Files with no reviewable changes (1)
- recipes/racon/racon_wrapper.patch
🔇 Additional comments (3)
recipes/racon/build.sh (1)
17-21: LGTM! Proper macOS build configuration.
The Darwin-specific configuration correctly disables framework and bundle searches, which is essential for clean builds on macOS systems.
recipes/racon/meta.yaml (2)
9-9: LGTM: Build number increment is appropriate
The build number increment is correct for adding arm64 support.
46-49: Verify the added identifiers
Please verify that Racon is actually registered in both biotools and Galaxy EU.
| arm64) | ||
| SPOA_OPTS="-Dspoa_optimize_for_portability=ON" | ||
| ;; |
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💡 Codebase verification
Architecture detection pattern needs to be updated for arm64 support
The codebase analysis reveals that the current implementation in recipes/racon/build.sh is inconsistent with the established patterns across other Bioconda recipes. Several key observations:
- Many recipes (e.g., wfa2-lib, vcf-validator, spacepharer) use
aarch64 | arm64pattern to handle both Linux and macOS ARM architectures in a single case - The SPOA options in racon should align with its dependency spoa's configuration (recipes/spoa/build.sh)
- The current implementation might miss optimizations for macOS ARM (arm64)
Suggested changes:
- Combine arm64 and aarch64 cases to use the same SIMDE configuration
- Match the pattern used by other recipes:
aarch64 | arm64)
🔗 Analysis chain
LGTM! Architecture-specific optimization correctly configured.
The arm64 case (Apple Silicon) appropriately uses portability optimization, distinct from the aarch64 (Linux ARM64) configuration. This aligns with platform-specific best practices.
Let's verify the architecture detection logic:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify architecture detection patterns in other bioconda recipes
# Expected: Find similar architecture detection patterns in other recipes
# Search for similar architecture detection patterns
rg -A 5 "case.*uname -m.*in"
Length of output: 11438
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