> I am trying to upgrade cufflinks version from 1.3.0 to 2.0.2. I changed the 
> directory in the PATH to version 2.0.2 but when I run cuffdiff on the galaxy 
> it still uses the version 1.3.0. Do I need to change the code of the wrapper?

This is the right approach, but there must be a glitch somewhere. If you're 
running Galaxy on a cluster and/or via a dedicated user, you'll want to set the 
PATH accordingly. For debugging, you could try echoing the path in the tool 

> Another question is how to I enable both version of cufflinks to appear and 
> run on the galaxy?

This isn't possible now but will be in the future when Cufflinks is moved to 
the tool shed.

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