I'm trying to run Tophat2 on a local instance of galaxy. Tophat2 and Bowtie 2 have been installed from the toolshed. I'm using a custom genome, which has been uploaded to the history. I've also uploaded the read files into the history (using the data library function - and we tried both just linking to the files, and copying the data into galaxy.) When I run Tophat2, it just immediately changes to complete, and all the resulting files are empty.
Any ideas on what may be going wrong? Are we missing some necessary tool?