Question: Tophat Problem On A New Local Instance
0
Elwood Linney • 180 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