---------- Forwarded message ---------- From: Yuri Bendana <yrbendana@gmail.com> Date: Wed, Dec 9, 2009 at 2:39 PM Subject: Re: [galaxy-dev] how to add genome build? To: Greg Von Kuster <greg@bx.psu.edu> 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 _______________________________________________ galaxy-dev mailing list

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