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
Hope to help you.
From: Gerald Bothe
Date: 2013-08-01 01:16
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?
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