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.
Genaro,
My question is which are the best/appropiate TOPHAT and CUFFDIFF versions?
Galaxy wrapper versions do not match tool versions. The tag 'requirements' will eventually be used to specify versions, but this work is not yet complete. You should use Tophat v1.4.0 or 1.4.1 and Cufflinks v1.3.0 for now.
The error message I get is TOPHAT not recognized.
To solve this problem, you'll need to install Tophat and add it to your Galaxy user's path
Any other suggestions?
Please send questions about local Galaxy installs to galaxy-dev rather than galaxy-user; galaxy-user is for questions about how to use Galaxy for bioinformatics analyses. Thanks, J.
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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participants (3)
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Genaro Pimienta -
Jennifer Jackson -
Jeremy Goecks