I'm running tophat2 like this on my newly installed galaxy:
(parameters not shown are just the defaults)
And I'm getting this error:
Error in tophat:
tophat: option --transcriptome-mismatches not recognized
for detailed help see http://tophat.cbcb.umd.edu/manual.html
I don't understand why the option is offered in the galaxy UI if it's
not available, or is there some kind of bug, or wrong version of
I'm on TopHat v2.0.6.
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