You can upload the required genome into your history and then from the "Use a built in reference genome or own from your history:" dropdown choose "use a genome from history" option of the Tophat tool. Tophat will then run using the desired reference genome.
BTW, these types of questions are best asked on the Biostar Q&A site for Galaxy (https://biostar.usegalaxy.org/) or the user mailing list (CC'd). That will give you better exposure to the community and hence a better chance for an answer.
Hope this help, Enis
On Sat, May 24, 2014 at 9:43 AM, shiny shishishiny@foxmail.com wrote:
Hello,Enis Afgan. I wonna run TOPHAT through the Galaxy project.Well, I can't find the reference genome of *Carica papaya.*So should I ask for help as it shows on the website,or it is easier should I turn to use Linux shell for me? Shiny