Hi Jen and James, Thanks for your info. Yes, we are already running a cloud instance ( http://galaxyclass.genenetwork.org/). So if I can build the index for colorspace, then how to configure it? And I didn’t find the “tophat_indexes_color” record in the Admin - “View data tables registry”. Please see attachment.
Lei Yan Center for Integrative and Translational Genomics The University of Tennessee Health Science Center On Wed, Oct 16, 2013 at 2:35 PM, James Taylor <ja...@jamestaylor.org> wrote: > They are already running a local instance. > > I didn't realize that bowtie required a different index for colorspace > alignment. So Lei, you will have to build the index using bowtie-build > -C. > > -- > James Taylor, Associate Professor, Biology/CS, Emory University > > > On Wed, Oct 16, 2013 at 3:31 PM, Jennifer Jackson <j...@bx.psu.edu> wrote: > > 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 > > >
<<attachment: 2013-10-16 02-54-06 PM.png>>
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