Thanks Jen and James so much.

Now it looks like I have fixed the problem about tophat_indexes_color, because "Tophat for SOLiD" tool is running in my account (still running, but not finished yet). Here is a summary:

The hg19 index files for colorspace have been there, so I don’t need to build or download.

/mnt/galaxyIndices/genomes/Hsapiens/hg19/bowtie_color/hg19

Change the tool_data_table_conf.xml file, add this:

< <table name="tophat_indexes_color" comment_char="#">

< <columns>value, dbkey, name, path</columns>

< <file path="/mnt/galaxyIndices/galaxy/tool-data/bowtie_indices_color.loc" />

< </table>

/mnt/galaxy/galaxy-app/tool_data_table_conf.xml

Yes, both Bowtie and Tophat use the same indexes.

bowtie_indexes and tophat_indexes use this loc file:

/mnt/galaxyIndices/galaxy/tool-data/bowtie_indices.loc

bowtie_indexes_color and tophat_indexes_color use this loc file:

/mnt/galaxyIndices/galaxy/tool-data/bowtie_indices_color.loc

Hope this can help somebody.

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

On Wed, Oct 16, 2013 at 3:21 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:

Hi Lei,

You can download all at once or in two parts (for slower connections):

iGenomes has been pretty good about using the exact same build as released by the source with no changes for the GTF files, but I do not know about the indexes - so do a test run once in place. Just to let you know, creating these may be easier than downloading, is just a single line command and you have a server to run this on, but the choice is yours.

Jen
Galaxy team
On 10/16/13 1:11 PM, Lei Yan wrote:

Hi James,

I found this: http://bowtie-bio.sourceforge.net/manual.shtml

There are some Pre-built indexes in the right side of this page.

If I just need an hg19 index for colorspace, which index file can work for us?

Thanks again.

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
>
-- 
Jennifer Hillman-Jackson
http://galaxyproject.org