Hi Ken,

You will need to install Cuffmerge and then link it in the same way that the other tools were added. This wiki has details: a link to the dependencies (versions) and how to configure paths/ENV set up:


If you need more help, please let us know. Please be sure to keep the galaxy-dev list on the cc - this group is great at troubleshooting local install issues.


Galaxy team

On 9/18/12 8:40 AM, Kenneth R. Auerbach wrote:
Hi Jen,

I have another question. Right now we have some RNA Analysis tools
(cufflinks, cuffdiff, and cuffcompare) but not cuffmerge. Can you tell
me how I would add it to the NGS:RNA Analysis group in our Galaxy

Thank you.

Jennifer Jackson
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