Please be aware that the GATK tools wrapped for Galaxy, all versions, whether from the Tool Shed or still hosted on a public server, are considered deprecated and are no longer supported. This means that any might not install correctly or fail for odd reasons. The GATK Data Managers intended to install built-in indexes on a local Galaxy are known to not function correctly.
The Galaxy variant analysis tutorials cover alternative tools/workflows: https://galaxyproject.org/learn/
That said, some GATK tools may still function. To use a custom genome, set the first option on the tool form Choose the source for the reference list as History. All datasets with the
fasta datatype assigned will then show up in the Using reference file option select list.
How to make sure a custom genome is formatted correctly:
- General help for all tools: https://galaxyproject.org/learn/custom-genomes/
- Specific help for GATK (older, may or may not still work for all use-cases): https://biostar.usegalaxy.org/p/14777/
Thanks! Jen, Galaxy team