It sounds like the reference genome is not set up for the Tophat tool.  Please have a look at the instructions (http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup) under "Tools and Their Corresponding loc Files" and "Bowtie and Tophat".


From: Rainy Luo <xiaolin2082@gmail.com>
Date: Monday, July 22, 2013 1:33 PM
To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Subject: [galaxy-dev] Problems with tophat in local instance

I am a beginner of Galaxy.Because I need to analyze large-scale NGS data and the pubic Galaxy serve did not work out,I installed linux(the first time to use linux) and set up the local galaxy instance in my computer. It seemed everything worked fine until I tried to use Tophat to align the reads to the reference genome.The problem is although I have already downloaded the Refgenome from UCSC,when I use the Tophat,"select a reference genome"option is empty(please see the attached file).
is there anybody having similar problem?How to deal with it?