Hello Rodolfo, I've cc'd the galaxy-dev mailing list as others may benefit from this exchange. On Nov 4, 2009, at 12:12 PM, Rodolfo Aramayo wrote:
Hi Greg,
Thanks for replying. No we are not running into any problems with Galaxy. In fact we LOVE IT! And students are asking to learn more about it. In fact we had a little coup in here because students refused to accept yet another Genomics Unix project, instead they requested projects in Galaxy.
This is great - so glad to hear this!
Anyway, the reason I was contacting you guys is to ask guidance into how to go about to load genomes that are not part of the current Galaxy set up into Galaxy. For example I would like to know what tables I would need to create for the genomes in question and how to link them to MySQL.
We are in the process of streamlining the process for supporting new genomes, but the current process is fairly simple. New database changes are needed. Since you are running your own local installation of Galaxy, new genomes can be specified by modifing the ${GALAXY_ROOT}/tool-data/shared/ucsc/builds.txt file. This file is generated using a script found at ${GALAXY_ROOT}/cron/updateucsc.sh. If this script is executed on a regular basis ( via cron perhaps ), 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.
I have installed Galaxy locally without problems and activated the EMBOSS part BUT, it is not clear to me how exactly go about making Galaxy talk to MySQL. Any help in this area would be GREATLY appreciated.
Hooking up Galaxy to and installed postgres or mysql database is simply a config setting in universe_wsgi.ini ( look for the following section in this file in your galaxy root install directory ). The URL you'll use depends on the name and location of your database and the security you've implemented, but for mysql could look something like the following. See the mysql docs for details [app:main] # Specifies the factory for the universe WSGI application paste.app_factory = galaxy.web.buildapp:app_factory # By default, Galaxy uses a SQLite database found here #database_file = database/universe.sqlite # You may use a SQLAlchemy connection string to specify an external database # instead. PostgreSQL and MySQL are supported. database_connection = mysql://greg_test?unix_socket=/var/run/mysqld/ mysqld.sock
Among other things, I am the director of the Laboratory for Genome Bioinformatics here at Texas A&M University and I have been training students in Bioinformatics/Genomics. I have access to very skillful undergraduate students who are very computer savvy and are itching to help Galaxy. We know a bit about Unix and MySQL but are not real experts...
Any help in this area would be great and would allow us to load the fungal genomes we want to study into Galaxy
Thanks for your help
Rodolfo
On Wed, Nov 4, 2009 at 09:12, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Rodolfo, Can you clarify what you would like to do? Are you running your own local Galaxy instance, or are you using our main public instance? Are you having problems uploading the files? Greg Von Kuster Galaxy Development Team
On Oct 26, 2009, at 4:29 PM, Rodolfo Aramayo wrote:
Hi, I teach Genomics and want to use Galaxy as a tool. I would like to upload a series of fungal genomes for this analysis. Who should I contact to talk about this? In other words, I need the name of a person who might help us or gude us through this process. Thank You for your help Rodolfo Aramayo, PhD Biology/Genetics Texas A&M University
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu