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
# 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
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 Von Kuster
Galaxy Development Team