augustus: add linux-aarch64 build #47056
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The Linux ARM64 build fails due to: |
bioconda/bioconda-recipes#47056 (comment) Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
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The Linux ARM64 build now fails due to:
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Needed by bioconda/bioconda-recipes#47056 (Bioconda/augustus) Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
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Oops, I jumped the gun on this on and thought perl-encode had already been built. |
📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces several changes to the Possibly related PRs
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Actionable comments posted: 1
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recipes/augustus/meta.yaml (1)
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1-169: Summary of review and next stepsOverall, the changes in this PR align well with the stated objectives of adding support for the Linux ARM64 architecture and updating the Augustus package. Here's a summary of the key points and next steps:
- The build number increment and addition of
run_exportsare appropriate and approved.- The version specifiers for samtools and bamtools need to be corrected from
=>to>=.- The addition of linux-aarch64 platform support is approved, but needs verification of the build process.
- The version update and SHA256 checksum change are approved, but the checksum should be verified.
Next steps:
- Make the suggested correction to the version specifiers.
- Run the provided verification scripts to ensure the package builds correctly on linux-aarch64 and the SHA256 checksum is correct.
- Address any issues that may arise from the verification process.
- Once these steps are completed, the PR should be ready for final review and merge.
Given the significant version bump for samtools (from 0.1.19 to 1.19), it would be prudent to thoroughly test Augustus with this new version to ensure there are no compatibility issues. Consider adding or updating tests that specifically exercise the samtools integration.
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recipes/augustus/meta.yaml (3)
16-18: LGTM: Build number increment and run_exports additionThe build number increment and the addition of the
run_exportssection are both appropriate changes:
- Incrementing the build number ensures that the new package will be recognized as a newer version by conda.
- The
run_exportssection with{{ pin_subpackage('augustus', max_pin="x") }}ensures that packages depending on augustus will use a compatible version, preventing potential ABI breakage issues.These changes align well with Bioconda best practices and the PR objectives.
168-169: LGTM: Addition of linux-aarch64 platform supportThe addition of 'linux-aarch64' to the 'additional-platforms' section in the 'extra' metadata is correct and aligns with the PR objective of adding support for the Linux ARM64 architecture.
To ensure that the package builds correctly on the new platform, please run the following verification script:
#!/bin/bash # Description: Verify that the package builds successfully on linux-aarch64 # Test: Check if the package builds on linux-aarch64 conda build --output-folder . .This script will attempt to build the package and will help identify any potential issues specific to the linux-aarch64 platform.
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1-2: LGTM: Version update and SHA256 checksum changeThe update of the package version to 3.5.0 and the corresponding SHA256 checksum change are consistent with a new release of Augustus. This is a good practice to ensure the integrity of the downloaded source.
To ensure the integrity of the source, please verify the SHA256 checksum using the following script:
This script will download the source tarball and verify its checksum against the one provided in the recipe.
recipes/augustus/meta.yaml
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| - samtools =>1.19 | ||
| - bamtools =>2.5.2 |
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Update version specifiers for samtools and bamtools
The version updates for samtools and bamtools are notable:
-
The samtools version has been significantly bumped from 0.1.19 to 1.19. This is a major version change that may introduce compatibility issues. Please ensure that Augustus is compatible with this newer version of samtools.
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The specific version requirement for bamtools (=>2.5.2) is good for reproducibility.
However, there's an issue with the syntax of the version specifiers:
The => operator is not a standard conda version specifier. Instead, use the >= operator for "greater than or equal to". Please update the lines as follows:
- samtools >=1.19
- bamtools >=2.5.2This change will ensure that conda correctly interprets the version requirements.
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