Hello Yuri,

The Extract Genomic DNA tool uses the alignseq.loc file in the ~tool-data directory for finding the builds.  This is a tab-delimited file that points to either alignment data or sequence data.  You should add something like

seq mt3 /opt/local/var/genome/mt3

( tab delimited )

to your local copy of this file, and the tool should work with this build.

To ensure fast response to questions like this, please send to the distribution list rather than my personal email address.


On Dec 9, 2009, at 5:39 PM, Yuri Bendana wrote:

Hi Greg,

I modified builds.txt for now and added:

mt3 Medicago truncatula v3

It now appears in the dropdown, great!  I also have this in faseq.loc:

mt3 /opt/local/var/genome/mt3

This is the directory where my genome fasta files are located.  However when I try to get sequence from the genome using the Extract Genomic DNA tool, I get this error:

"Sequences are not currently available for the specified build."

No other errors appear in paster.log.  What am I missing?

thanks,

yuri

On Tue, Dec 8, 2009 at 10:40 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Yuri,

You are correct, new genomes can be specified by modifing the ${GALAXY_ROOT}/tool-data/shared/ucsc/builds.txt. This file is generated using a script found at ${GALAXY_ROOT}/cron/updateucsc.sh.  If this script is executed on a normal basis, it will be useful to instead add the required information to ${GALAXY_ROOT}/tool-data/shared/ucsc/manual_builds.txt before running the script (otherwise each time the script is run, the changes to build.txt will be lost). See ${GALAXY_ROOT}/cron/README.txt for more information as well as the headers of each data file.



On Dec 2, 2009, at 9:54 PM, Yuri Bendana wrote:

I recently installed Galaxy and am pleasantly surprised how easy it is to get up and running.  The screencasts and wiki are very helpful. One thing I can't figure out is how to add a Medicago genome to the Database/Build dropdown that appears when I try to edit my query attributes (it looks like the same builds appear in the Genome dropdown on the Get Data->Upload page).  I thought adding the genome directory to the tools-data/faseq.loc file might work but doesn't seem to. I noticed that the build list displayed is stored in tool-data/shared/ucsc/builds.txt and it looks like it gets updated by a cron script. I would like to use the Fetch Sequences -> Extract Genomic DNA tool on my local genomes.

thanks,

yuri
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Greg Von Kuster
Galaxy Development Team
greg@bx.psu.edu





Greg Von Kuster
Galaxy Development Team
greg@bx.psu.edu