When using RNA STAR in the past, I’ve been able to select from many built-in genomes as a reference. However, under the “select reference genome” I only see “No options available.” This occurs if I select with or without a built-in gene model. If anyone can give me any tips on how to find a way to select a reference genome (I only need mm10 and hg38) it would be much appreciated!
We were able to confirm the issue.
A ticket to get this resolved has been created and can be found here: https://github.com/galaxyproject/usegalaxy-playbook/issues/292
A test to see if an earlier version of the tool will work is in progress. You could also test it out. Using usegalaxy.eu instead is another short-term option.
The ticket above has the details for everything mentioned. The ticket will update as more workarounds are confirmed and/or the tool itself is reconfigured to locate the indexes properly.
Thanks for reporting the problem!