Question: Tophat Problem On A New Local Instance
gravatar for Elwood Linney
5.5 years ago by
Elwood Linney180
Elwood Linney180 wrote:
I have installed a local instance of Galaxy as a one user in a Mac Pro desktop. I got some valuable help from Dannon Baker regarding how to load large datasets into it. However I noticed that the Upload file for this instance would only go up to the Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) version of the zebrafish assembly while where as the online version went up to the newer assembly zebrafish assembly Jul. 2010 (Zv9/danRER7) While I could download newer reference genome in the program from UCSC Main table browser whenever the local instance offered alternatives for genomes it only went up the earlier version (Zv8/danRer6) (danRer6) . I went ahead anyway, groomed 4 x 16gb datasets but when it came to Tophat, An error occurred with this dataset: Could not determine Tophat version /bin/sh: tophat: command not found Error indexing reference sequence /bin/sh: bowtie-build: command not found Also, when I download from UCSC the most updated zebrafish genome reference sequence and use it for Tophat, I get the following error signal: I don't know if this issue of assembly version is associated with my Tophat problem--the two Tophat screens I get from either the main Galaxy or my instance are attached for comparison: my local instance does not give me a "Use built-in genome option" while the main Galaxy does Any advice? Elwood Linney DUMC
alignment bowtie • 901 views
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