Regarding (2), have you installed bowtie and tophat on your Mac Pro? Galaxy does not currently automatically install all of the software needed to run tools (we are working on this through the toolshed, but at the moment it is a manual process). Dependencies of various tools included in the distribution are here: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jun 11, 2013 at 9:20 AM, Elwood Linney <ellinney@gmail.com> wrote:

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

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