Re: [galaxy-dev] tophat: option --transcriptome-mismatches not recognized

14 Dec 2012


      I'm thinking this must be a bug.  When I look at the options for
tophat I don't see "--transcriptome-mismatches" mentioned.

-Greg

On Fri, Dec 14, 2012 at 10:04 AM, greg <margeemail@gmail.com> wrote:
...
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