You can overwrite your copy of the Cuffdiff wrapper at 
tools/ngs_rna/cuffdiff_wrapper.xml with the new version:

https://bitbucket.org/galaxy/galaxy-central/raw/48fad71361b3075c85c7d365dd52c106cabad73a/tools/ngs_rna/cuffdiff_wrapper.xml

Best,
J.

On Sep 16, 2013, at 5:36 PM, Matthew Paul wrote:

> Hey Galaxy,
> 
> I am trying to use CuffDIff with replicate analysis on a local instance. I 
> saw that Jeremy Goecks had a solution to this problem: 
> http://user.list.galaxyproject.org/Cuffdiff-changes-tt4655893.html#a4655901.
> Could I see/use this source code please? I can't really wait until the next 
> update.
> 
> Thanks,
> Matt Paul
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