"Best practice" for maintaining genome list in Galaxy

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"Best practice" for maintaining genome list in Galaxy

Peter van Heusden
Hi there

Is there current "best practice" for maintaining a collection of reference genome data in a Galaxy server? I.e. filling in the dbkeys.loc and all_fasta.loc table and associated data. I know of the following discussions on this topic:

3. This biostars answer: https://biostar.usegalaxy.org/p/7176/
4. This page on custom genomes that seems to be user / history oriented: https://galaxyproject.org/learn/custom-genomes/
5. This page on rsyncing from the Galaxy reference data collection: https://galaxyproject.org/admin/use-galaxy-rsync/ - quick test gives me rsync error though
6. This guide to using the human reference data: https://biostar.usegalaxy.org/p/14777/
7. I hear the usegalaxy.org reference collection is available via cvmfs - I think this was discussed in a Galaxy Admins meetup at some point.

None of this is comprehensive. There are 2 sets of questions for me (in my role as Galaxy admin):

1. If I want to make reference genomes and common indices (like for HISAT and BWA) available for e.g. human and mouse, what is the best way to do this?

2. If I want to add a genome for a non-model organism (e.g. M. tuberculosis or L. calcarifer) available, what is the best way to do this? Which data manager should or could I use?


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