I'm running tophat2 like this on my newly installed galaxy:
http://snag.gy/OfLND.jpg
(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
tophat2?
I'm on TopHat v2.0.6.
Thanks,
Greg
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