Update lofreq to add bcftools dependency #51672
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🧹 Outside diff range and nitpick comments (2)
recipes/lofreq/meta.yaml (2)
42-42: Consider adding more specific bcftools tests.While
bcftools --helpverifies the basic installation, consider adding tests that verify the specific bcftools functionality required bylofreq call-parallel.Example test to consider adding:
test: commands: - lofreq version - samtools --help - bcftools --help + - lofreq call-parallel --help
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14-35: Consider using run_exports in bcftools package instead.Since bcftools is now a critical dependency for lofreq's functionality, consider working with the bcftools package maintainers to add appropriate
run_exportsin the bcftools package itself. This would automatically manage version constraints for all dependent packages.
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recipes/lofreq/meta.yaml (2)
14-14: LGTM: Build number increment is appropriate.The build number increment is correct for adding a new dependency while keeping the same version.
35-35: Consider adding version constraints for bcftools.While adding bcftools as a dependency is correct, consider specifying a minimum version requirement to ensure compatibility.
Let's verify how bcftools is used in the codebase:
#51417 introduced additional post-2.1.5 development changes to lofreq 2.1.5. These included a new dependency on bcftools, which was not a dependency of the package. Without this dependency the current build of lofreq is broken for all invocations of
lofreq call-parallel.Please read the guidelines for Bioconda recipes before opening a pull request (PR).
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If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
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