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Add pod5 container

Open eperezme opened this issue 1 year ago • 3 comments

Submitting a Container

Check BioContainers' Dockerfile specifications

Checklist

  1. Misc
  • [x] My tool exists in BioConda but doesn't have a container
  • [x] The image can be built
  1. Metadata
  • [x] LABEL base_image
  • [x] LABEL version
  • [x] LABEL software.version
  • [x] LABEL about.summary
  • [x] LABEL about.home
  • [x] LABEL about.license
  • [x] MAINTAINER
  1. Extra (optionals)
  • [ ] I have written tests in test-cmds.txt
  • [x] LABEL extra.identifier
  • [x] LABEL about.documentation
  • [x] LABEL about.license_file
  • [x] LABEL about.tags

Check BioContainers' Dockerfile metadata

eperezme avatar Oct 09 '24 11:10 eperezme

I believe there is already a docker image for pod5 (and a conda package)

https://bioconda.github.io/recipes/pod5/README.html#package-pod5 https://quay.io/repository/biocontainers/pod5?tab=tags

Is there any issue with this image?

Edit: Ah, the 'procps' package maybe?

mboudet avatar Oct 09 '24 13:10 mboudet

There was some error with the vbz_h5py_plugin: POD5 has encountered an error: 'No module named 'vbz_h5py_plugin"

Edit: I also had to install on my pc the pod5 package throught pip bc the conda package was giving me errors

eperezme avatar Oct 09 '24 13:10 eperezme

Might be worth to raise the issue with the package maintainer, as conda should include all required dependencies.. I'd rather not have a separate docker image for the same software just because of a bug.

(if they do not want to fix it, I'll merge this PR)

mboudet avatar Oct 09 '24 13:10 mboudet