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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