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@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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