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

On Wed, Oct 16, 2013 at 2:54 PM, Lei Yan <leiyan2000@gmail.com> wrote:

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 <james@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 <jen@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-dev@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
>