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
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
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?
The parameter has been deprecated in recent versions of Tophat; the wrapper has been updated in -central changeset 4b4ea9952336 to reflect this.
J.
Thanks. So I should just wait for that changeset to make it into the stable release and update my code?
When could I let my users know to expect that? I think they'll just use command line tophat until then.
-Greg
On Fri, Dec 14, 2012 at 2:41 PM, Jeremy Goecks jeremy.goecks@emory.edu wrote:
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?
The parameter has been deprecated in recent versions of Tophat; the wrapper has been updated in -central changeset 4b4ea9952336 to reflect this.
J.
Thanks. So I should just wait for that changeset to make it into the stable release and update my code?
If you're comfortable with Mercurial, you can apply the individual changeset and merge later.
When could I let my users know to expect that? I think they'll just use command line tophat until then.
The next distribution is scheduled for 12/20.
J.
galaxy-dev@lists.galaxyproject.org
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greg -
Jeremy Goecks