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Add gatktool to conda env for CNNScoreVariants #1786
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By the way, @FriederikeHanssen , do you know why this module uses the official container |
Yes because I could never get the biocontainers one too work because of the missing dependency in the conda package. Didn't think about building a mulled container at that point 🙈 I think I opened an issue somewhere to fix the conda recipe. Seems like using a mulled one would be a good solution though. |
Oki. I'll give the mulled container a try 🤞🏼 |
Can't find it on bioconda: https://github.com/bioconda/bioconda-recipes/issues?q=is%3Aissue+gatk4+ |
@FriederikeHanssen I misread the CI, and actually the test is still failing on Conda despite your change. I didn't have to try a mulled container at all ! Here is the error log:
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lol I checked this on my phone this morning and didn't see that this was my PR. But it stands: I could never get it to work and eventually gave up. 😆 Found the issue I had in mind: broadinstitute/gatk#7811 |
thanks for picking this up again, I completely forgot about this PR. This one would have benefited from being nagged by an i-am-stale-please-take-care-of-me-bot 😆 |
OK. I'll close this PR and open an issue instead |
PR checklist
Closes #XXX
versions.yml
file.label
PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware