Hopefully you have discovered this already, but public Galaxy servers usually do not include indexed reference annotation.
For the reference genome, try one of these:
Use an available build-in reference genome index without annotation.
fastafile from the history that represents the reference genome.
For the reference annotation, try:
- Use a matching reference annotation provided by you from the history.
GTFwill work best with this tool and many others.
FAQs. Skip the first three and just review the last one if using a built-in genome index.