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Should EDAM tool panels use bio.tools defined EDAM terms? #19356

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bernt-matthias opened this issue Dec 20, 2024 · 1 comment
Open

Should EDAM tool panels use bio.tools defined EDAM terms? #19356

bernt-matthias opened this issue Dec 20, 2024 · 1 comment

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@bernt-matthias
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Describe the bug

If I got it right EDAM terms should be derived from bio.tools: #12291?
Currently this seems not to work. I checked for a few tools on usegalaxy.eu/org (e.g. megahit, dada2) and despite having a bio.tools entry in the sool source the tool is shown as uncategorized.

Galaxy Version and/or server at which you observed the bug
Galaxy Version: 24.0-24.2

To Reproduce

  1. Check EDAM tool panel sections for a few tools.

Expected behavior

Tools with bio.tools annotation should be used.

@jmchilton
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It should but reviewing that PR all that is optional. The naive approach of using the API can be configured but that would result in thousands of API calls during Galaxy's startup which is already so slow. Someone needs to configure the content directory options in that PR I think. It would be awesome if that was just part of the Galaxy Ansible role I guess. We also have cron-style tasks now - it might make sense to have Galaxy manage that.

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