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.


On Fri, Dec 14, 2012 at 2:41 PM, Jeremy Goecks <> 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.
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