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
#2222
Salt Lake City, UT 84108
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___________________________________________________________
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
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