[galaxy-user] Galaxy local install problems understanding where to put mouse ref seq data to populate ref genome in BWA

Jennifer Jackson jen at bx.psu.edu
Wed Nov 9 18:11:36 EST 2011


Hello Christopher,

This wiki explains the exact steps for how to set up reference genomes 
for NGS tools, including BWA:
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

Please let us know if you have any questions. For local instance 
questions, searching prior answers (Nabble) or posting to 
galaxy-dev at bx.psu.edu is recommended.
http://galaxyproject.org/wiki/Mailing%20Lists

Take care,

Jen
Galaxy team

On 11/9/11 11:02 AM, Christopher Callaway wrote:
> Hello,
>
> I am still having problems understanding how to install mm9 mouse ref
> genome into our own install of Galaxy. When I try to map with BWA for
> Illumina the drop down for select ref genome is not populated with
> anything. How do you grab the mm9 ref file and how do you convert it so
> that Galaxy local “sees” it? How do you build the index and how do you
> prepare the loc file? Our install does not contain a folder
> tool-data/shared/ucsc/builds.txt.
>
> Sorry but I am not a programmer, just a bench scientist.
>
> Thanks in advance,
>
> Christopher W. Callaway
>
> University of Utah
>
> Dept. of Pediatrics
>
> Division of Neonatology
>
> 417 Wakara Way
>
> #2222
>
> Salt Lake City, UT 84108
>
>
>
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-- 
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support


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