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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