Hello, I will try this again without attachments and hope it gets on the list.
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
So minimally I have two problems that may or may not be related:
1)The Galaxy-dist that I just installed into a Mac pro does not have the latest zebrafish assembly
2) but more importantly when I try to process groomed datasets through Tophat and "Use a built-in genome" as reference it does not allow me an option for the reference genome AND if I try to use a reference genome from the UCSC download, it won't allow that.
So right now I am stymied--any advice?
Elwood Linney Duke University Medical Center