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 <j...@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 <leiyan2...@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 <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
>>> >
>>>
>>
>>
>
> --
> Jennifer Hillman-Jacksonhttp://galaxyproject.org
>
>

<<dggddfba.png>>

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