Tophat doesn't seem to be executing on usegalaxy.org. The jobs are being queued, but they haven't started running after several hours. I've tried several different settings (paired-end vs single-end, precomputed reference vs fasta file) - nothing seems to be running.
Is this a server load problem or is there an issue with Tophat?
Update: Tophat jobs do run eventually - my bad! It just takes a few hours before they execute. I presume there must be some minimum processor number or memory requirement for Tophat that delays these jobs on the Galaxy server?