> 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 to
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 wrote:
>> I don't understand why
> 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
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 wrote:
> I'm running tophat2 like this on my newly installed galaxy:
> http://snag.gy/OfLND.jpg
> (parameters not shown are jus
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
