I recently moved out production galaxy from one postgres database to another. In the process I can no longer access the custom genomes added in our tophat .loc file. I attmepted to reload the file using local data however it is not seeing the genome indices.
It could be that not all of the files associated with genome indexes were migrated to the new database. Or, that the file paths within the files are no longer valid for the new database location. Check those two items first if this is still an issue.
Thanks, Jen, Galaxy team