Reference genomes aren't distributed along with the galaxy source due to size 
and other factors, but we do have a walkthrough for setting it all up on the 
wiki at http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup, see the Setting up 
References section.

Thanks!

Dannon

On Oct 25, 2011, at 5:31 PM, Christopher Callaway wrote:

> Hi,
>  
> I have Galaxy running locally and when trying to BWA map a set of paired-end 
> reads, the reference genome does not show up (mm9) by selecting either 
> History or Built-in.  How do I fix this?
>  
> Thanks,
>  
> 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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