Hi Genaro,

For reference, these are the tool version recommended for use with local installs: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies

for Bowtie, the supported version is 0.12.7 for Tophat, the supported versions are 1.3.3-1.4.0 for Cufflinks/merge/diff, the supported version is 1.3.0

Using a supported version of these tools should resolve the issues you are having. However, if you continue to have problems. please feel free to write back. The best list to send questions about local installs to is the galaxy-dev@bx.psu.edu mailing list: http://wiki.g2.bx.psu.edu/Support#Mailing_Lists

Best, Jen Galaxy team

On 2/25/12 7:27 AM, Genaro Pimienta wrote:

Dear all: I have GALAXY installed in a UNIX server. BOWTIE works fine but TOPHAT and CUFFDIFF crash upon starting. In the case of TOPHAT, I noticed that GALAXY has a 1.5.0 version integrated, while the TOPHAT website claims the latest version is 1.4.1. My question is which are the best/appropiate TOPHAT and CUFFDIFF versions? The error message I get is TOPHAT not recognized. Any other suggestions? Thanks, G.

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