I am able to run Tophat with both single and paired-end inputs without a problem on a few clusters (not all test jobs finished yet).
Update: There were issues with jobs running on the cluster Stampede yesterday. Perhaps avoid that cluster and use Jetstream instead.
If you need more help, please describe the error message and/or submit a bug report. https://wiki.galaxyproject.org/Support#Reporting_tool_errors
Thanks, Jen, Galaxy team