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 ( 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,

On Sat, May 24, 2014 at 9:43 AM, shiny <> 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
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