Question: Tophat Problem On A New Local Instance
0
Elwood Linney • 180 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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modified 5.5 years ago
by
James Taylor ♦ 470
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written
5.5 years ago by
Elwood Linney • 180
