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: http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies 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. Thanks! Jen 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 installation?

Thank you. Ken.

-- Jennifer Jackson http://galaxyproject.org