I am attempting to determine the best way to add a reference genome to STAR. Since there is no data manager and I would prefer not to have to use a fasta file for each run, what is the best method for adding the reference?
Create the indexes locally and edit the tool's associated "loc" file. The sample loc file with instructions is included in the tool's repository. For example (view is from the Tool Shed): RNASTAR Loc File Details
Hopefully this helps! Jen, Galaxy team