Make a new trim-galore build #51563
Make a new trim-galore build #51563
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/trim-galore/meta.yaml (2)
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17-21: Consider adding version constraints for dependencies.While the dependencies are listed correctly, there are no version constraints specified, particularly for cutadapt. The PR objective mentions incorporating a newer version of cutadapt with ARM compatibility. To ensure this, consider adding a minimum version constraint for cutadapt.
Example:
run: - perl - fastqc - cutadapt >=3.0 # Adjust this version as needed for ARM compatibilityAdditionally, consider adding version constraints for perl and fastqc to ensure compatibility and reproducibility.
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23-25: Consider enhancing the test command.The current test command verifies that trim_galore is installed and produces help output. While this is a good basic check, consider adding more comprehensive tests to ensure functionality. For example:
test: commands: - trim_galore --version - trim_galore --help | grep trim_galore > /dev/null - trim_galore --help | grep cutadapt > /dev/null # Ensure cutadapt is mentioned in the help outputThis would verify the version, basic help output, and the integration with cutadapt.
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🔇 Additional comments (3)
recipes/trim-galore/meta.yaml (3)
13-13: Build number increment looks good.The build number has been correctly incremented from 0 to 1, which is appropriate when updating a package. This change aligns with the PR objective to create a new build.
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27-40: Metadata looks good.The about and extra sections provide comprehensive metadata for the package, including the home URL, license information, summary, and relevant identifiers. This information appears to be complete and accurate.
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1-2: Verify SHA256 checksum for the new version.The version has been updated to 0.6.10, which aligns with the PR objective. Please ensure that the provided SHA256 checksum is correct for this new version.
To verify the checksum, you can run the following command:
Please compare the output with the checksum in the recipe to ensure they match.
recipes/trim-galore/meta.yaml
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| build: | ||
| number: 0 | ||
| number: 1 | ||
| noarch: generic | ||
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🛠️ Refactor suggestion
Consider adding a run_exports section.
To better manage dependencies and prevent potential API, ABI, and CLI breakage issues, consider adding a run_exports section to the build section. This would ensure that the dependency versions used at build time are recorded and locked. For example:
build:
number: 1
noarch: generic
run_exports:
- {{ pin_subpackage('trim-galore', max_pin='x.x') }}This addition aligns with the PR objectives and Bioconda best practices.
I'm mostly just after a new build in the biocontainer so it has a newer cutdapt, which have ARM compatibility in more recent conda versions.
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
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
"myrecipe"with eithernameif aname|lowervariable is defined in your recipe or with the lowercase name of the package in quotes.Bot commands for PR management
Please use the following BiocondaBot commands:
Everyone has access to the following BiocondaBot commands, which can be given in a comment:
@BiocondaBot please update@BiocondaBot please add labelplease review & mergelabel.@BiocondaBot please fetch artifactsYou can use this to test packages locally.
Note that the
@BiocondaBot please mergecommand is now depreciated. Please just squash and merge instead.Also, the bot watches for comments from non-members that include
@bioconda/<team>and will automatically re-post them to notify the addressed<team>.