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

2011-11-09 Thread Jennifer Jackson 

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-...@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

#

Salt Lake City, UT 84108



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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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[galaxy-user] Galaxy local install problems understanding where to put mouse ref seq data to populate ref genome in BWA

2011-11-09 Thread Christopher Callaway 
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
#
Salt Lake City, UT 84108

___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/