Hi,
I think you can get reference genomes from UCSC,and then make Bowtie2 index 
data by bowtie2-build.Other way you can try rsync to get the index files ,for 
more information you can see 
http://wiki.galaxyproject.org/Admin/Data%20Integration .
Hope to help you.




shenwiyn

From: Gerald Bothe
Date: 2013-08-01 01:16
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] reference genomes missing
I installed a local instance of GALAXY following the instructions at "Get 
Galaxy ..." in the Wiki. It installed ok, but when I tried the Bowtie2 mapper 
with a test data set, I noticed that the reference genomes are missing. How can 
I get the reference genomes (e.g. latest version of mouse and human) and 
integrate them into Galaxy? Or is there a Galaxy version available that has the 
genomes already installed?
Thanks

Gerald 

      
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