Update module template to support container registries#1991
Update module template to support container registries#1991edmundmiller wants to merge 19 commits intodevfrom
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Python linting (
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Codecov Report
@@ Coverage Diff @@
## dev #1991 +/- ##
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+ Coverage 62.01% 62.59% +0.58%
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Files 42 43 +1
Lines 4862 4898 +36
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+ Hits 3015 3066 +51
+ Misses 1847 1832 -15
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mahesh-panchal
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Seems the JSON schema is also missing the new param.
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Think we need to iron out how we get |
This isn't testing the creation of a new module, it's just checking that linting works in a new modules _repo_
This isn't as pretty as the biocontainers api for now, but it works and was recommended in the biocontainers gitter and is how galaxy pulls the images in. Useful links from the gitter: https://matrix.to/#/!wNQPhGTQvTINsnORJY:gitter.im/$8j7bYssM3ZqiMPLnqPQa5BMKjJppeQ_59H-5LVXkYo4?via=gitter.im&via=matrix.org https://github.com/galaxyproject/galaxy/blob/6da2f0e98cfd99b33b8fdb8d63f36096f477aa73/lib/galaxy/tool_util/deps/mulled/util.py#L225 https://github.com/galaxyproject/galaxy/blob/6da2f0e98cfd99b33b8fdb8d63f36096f477aa73/lib/galaxy/tool_util/deps/mulled/util.py#L18 https://github.com/common-workflow-language/cwltool/blob/main/cwltool/software_requirements.py
Co-authored-by: mahesh-panchal <[email protected]>
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| singularity_image = all_singularity[k]["image"] | ||
| current_date = date | ||
| return docker_image["image_name"], singularity_image["image_name"] | ||
| return response.json()["tags"][0]["name"] |
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I tried with hla-la and I get an older version than for bioconda. Should we check if versions match and downgrade bioconda if they don't?
conda (params.enable_conda ? "bioconda::hla-la=1.0.3" : null)
def container_image = "hla-la:1.0.1--h1b026d1_5"
container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
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Can you manually check if there's a matching hla-la version? I was just lazy and hoped asking it for only one image gave you the latest 😬
I can check that myself.
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Okay there is a 1.0.3 version, the problem is it got pushed 4 months ago, but the 1.0.1 version with the _5 build got pushed 3 months ago.
IDK what that's about, or which one we'd want to choose in that case.
https://quay.io/repository/biocontainers/hla-la?tab=tags
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Oh, I see that's an edge case. Then I guess we can let the user decide, but maybe still print a warning if the versions are different.
Co-authored-by: Júlia Mir Pedrol <[email protected]>
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I think this is now implemented, please reopen @edmundmiller if that is not the case |
PR checklist
CHANGELOG.mdis updateddocsis updatedDoes the prep work for nf-core/modules#2291