[galaxy-user] Galaxy local install problems understanding where to put mouse ref seq data to populate ref genome in BWA

Jennifer Jackson jen at bx.psu.edu
Wed Nov 9 18:11:36 EST 2011

Hello Christopher,

This wiki explains the exact steps for how to set up reference genomes 
for NGS tools, including BWA:

Please let us know if you have any questions. For local instance 
questions, searching prior answers (Nabble) or posting to 
galaxy-dev at bx.psu.edu is recommended.

Take care,

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
> ___________________________________________________________
> 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
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>    http://lists.bx.psu.edu/listinfo/galaxy-dev
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>    http://lists.bx.psu.edu/

Jennifer Jackson

More information about the galaxy-user mailing list