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:
http://wiki.galaxyproject.org/BigPicture/Choices
http://usegalaxy.org/toolshed
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:
http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance
http://wiki.galaxyproject.org/Admin/Data%20Integration
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
Hopefully this helps!
Jen
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
http://galaxyproject.org
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