2.8 years ago by
When you installed from the Tool Shed, did you use "managed dependencies" within the admin tool forms? Have you double checked the list of installed tools to see if there were any problems/the install was complete?
I realize that these seem obvious, but are sometimes easy to miss, especially if you have installed many tools.
The error is not exactly clear - but please be aware that this tool requires reference genomes and indexes to function. There are Data Managers in the Tool Shed for these functions. Be sure to create SAM indexes for every genome - many tools/functions reply on that content.
Thanks and let us know if this extra info does not help. We will need more details about your instance and the full error report/log to diagnose this further. Best, Jen, Galaxy team