Question: Tophat Version In Galaxy
gravatar for Genaro Pimienta
6.8 years ago by
Genaro Pimienta10 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.
alignment bowtie • 1.1k views
ADD COMMENTlink modified 6.8 years ago by Jennifer Hillman Jackson25k • written 6.8 years ago by Genaro Pimienta10
gravatar for Jennifer Hillman Jackson
6.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hi Genaro, For reference, these are the tool version recommended for use with local installs: 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 mailing list: Best, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 6.8 years ago by Jennifer Hillman Jackson25k
gravatar for Jeremy Goecks
6.8 years ago by
Jeremy Goecks2.2k
Jeremy Goecks2.2k wrote:
Genaro, 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. To solve this problem, you'll need to install Tophat and add it to your Galaxy user's path 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.
ADD COMMENTlink written 6.8 years ago by Jeremy Goecks2.2k
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