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_unin...

...

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

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_unin...

...

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

Lei Yan, I am very glad that this worked out! It looks like you have already helped at least one other user and I am sure others to come! We were discussing this internally while you were working. Updates to the ready-loaded data on cloud instances will be getting a make-over in the near term (this has been in planning for a while). Ease of data install for locals is included in the larger project goals. Technical implementation details are being sorted out to ensure the most robust solution, but data services that meet our project's three core goals of "accessible, reproducible, and transparent" are without question the central design criteria for success. Thank you again! We very much value the patience, tenacity, and time you took to not only see this through for yourself, but to post your experience & methods back to the list so clearly to share with others. Our community, most definitely including you, are so important. We are all "Galaxy team" :) Jen Galaxy team

Hope this can help somebody.

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

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