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.

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?