Hello Lei,

If genomes are not listed, that means that they are not indexed for use with the tool. The test server is primarily for demonstration or test use besides, and there could be other unexpected issues even if genomes are listed (we really do test here). Also, the quotas are very small (10G). If you want to use this tool, a local, cloud, or slipstream Galaxy is recommended. Full choices with details are listed here:

Help for setup is here, with the galaxy-...@bx.psu.edu mailing list available for further support. Tools will need to be installed, and indexes created. You can rsync the genome, but most genomes will not have loc file entries and indexes for SOLiD already created - see the Tophat manual for the command to create these:

Hopefully this helps!

Galaxy team

On 10/16/13 11:57 AM, Lei Yan wrote:
Hi all,

We are trying to use “Tophat for SOLiD”.
But this tool (Tophat for SOLiD) does not seem to be linked to the reference genomes that are installed. I can see those genomes on the Tophat for illumina tool and the other tools that require a reference genome. Please see attachments.
Does anybody have any ideas for this? Thanks a lot.

Lei Yan
Center for Integrative and Translational Genomics
The University of Tennessee Health Science Center

Jennifer Hillman-Jackson

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