Also check http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn which includes indices for Bowtie2 [see ftp://ussd-ftp.illumina.com/README.txt].
From: shenwiyn <shenwiyn@gmail.commailto:shenwiyn@gmail.com> Reply-To: shenwiyn <shenwiyn@gmail.commailto:shenwiyn@gmail.com> Date: Thursday, August 1, 2013 3:17 AM To: Gerald Bothe <g_bothe@yahoo.commailto:g_bothe@yahoo.com>, "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] reference genomes missing
Hi, I think you can get reference genomes from UCSChttp://http://hgdownload.soe.ucsc.edu/downloads.html,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 Bothemailto:g_bothe@yahoo.com Date: 2013-08-01 01:16 To: galaxy-dev@lists.bx.psu.edumailto: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