Specifying or using most recent bioconda build number for Seqera Containers

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Hello,

What would be the best way to specify (or take the most recent) bioconda build number for a bioconda recipe of a given version in seqera containers?

For specifics, I recently updated the vcf2maf v1.6.22 bioconda recipe from build 1 → 2 which needed some build options (and hence runtime behaviours) changed: added data directory where vcf2maf expects it (#60986) · bioconda/bioconda-recipes@469213d · GitHub

but from what I can tell from the Seqera singularity container build log, build 0 is the one getting downloaded instead of the most recent 2: Containers | Seqera.

(see the ‘_0’ on the line: https://conda.anaconda.org/bioconda/noarch/vcf2maf-1.6.22-hdfd78af_0.tar.bz2`` ...)

Am I misinterpreting which build is the one getting used for the container? Would there be a better way to check?

Thanks for the help.

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If you ever find yourself struggling with control or granularity when it comes to the Seqera Containers web interface, I always suggest trying with the Wave CLI. It’s Wave that powers Seqera Containers, and the CLI tool gives you complete control.

In this case, the command you’re after (taking the version identifier from the bioconda page) is as follows:

$ wave --conda vcf2maf=1.6.22=hdfd78af_2 --freeze
community.wave.seqera.io/library/vcf2maf:1.6.22--d429def261b20bac

Specifying --freeze without --build-repo tells Wave to save the image in the Seqera Containers community registry.

You can take the Wave build ID at the end of the container URI to get to the build status page if you’re interested:

Hope this helps!

Phil

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That’s great thank you! Small follow-up that I don’t think deserves it’s own topic (maybe I’m wrong):

Would there be a way to build nf-core-module required https:// singularity links with the Wave CLI?

It would be to update my PR which originally used Seqera containers: bump vcf2maf to ensembl-vep=113.4 and update containers by JustinBellavance · Pull Request #9515 · nf-core/modules · GitHub

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Yes there is, it’s just a bit awkward. You can do it via the CLI with wave inspect but the easiest is probably to use this script:

Also, that now you’ve built the new build via the CLI, maybe it’ll show up via the web interface? I’m not sure.

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