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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