Hi all,

Jeremy Goecks wrote, On 06/07/2011 01:25 PM:
> 
> If you modify the Cufflinks/compare/diff wrappers to be compatible
> with 1.0.2/3, please either put them in the toolshed or send them to
> me and I'll incorporate them into the Galaxy code base.
> 

We are actually working on customized version of those tools, with parameters 
which better suit our needs, I'm happy to share.
They are far from stable, so no tool-shed yet.

The XML's are here:
http://cancan.cshl.edu/labmembers/gordon/files/cshl_rnaseq_tools_2011-06-07.tar.bz2

They use Cufflinks 1.0.3, but also require a small patch to Galaxy (included in 
the tarball), to add our "$input.tag" labeling hack.
Without this patch, you'll need to modify the <output> labels and the "--label" 
parameter of cuffdiff (with this patch, it calculates the labels automatically).

See the working interface go here:
http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_cufflinks
http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_cuffcompare
http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_cuffdiff
http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_cuffdiff_replicates

Comments are always welcomed,
 -gordon

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