2.8 years ago by
Did you install the genome using a Data Manager from the Tool Shed? It sounds as if either the .len data or possibly another key index (samtools) is not present. On a local, be sure to use the Data Manager for installing a genome with a dbkey if it is not already in the default list. Then also create a 2bit, Samtools, and Picard index as the first steps before creating the Tophat indexes. If you need to start over, just use a slightly different dbkey for the genome.
Removing indexes that are already installed is very difficult (and manual). However, if the older index really needs to be removed, (in many cases not, instead consider just a adding a new one), it is recommended to instead start over with a fresh Galaxy instance, then install indexes using the correct data managers, in this order.
Thanks, Jen, Galaxy team