Configuring MySQL for Galaxy (and vice versa)
Dear Galaxy devs, I'd like to try a Galaxy installation with a database connection and have it use a freshly installed MySQL. It's a Kubuntu system where I just installed all needed packages, MySQL is up and running fine. In the Galaxy "universe_wsgi.ini" I commented out the sqlite entry and activated the one for a DB connection and it now shows now this: database_connection =mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock database_engine_option_echo = true database_engine_option_echo_pool = true database_engine_option_pool_size = 10 database_engine_option_max_overflow = 20 database_engine_option_pool_recycle = 7200 What I can't find in the online documents (Wiki) or via a Google search is: 1) how to tell Galaxy it should use a given MySQL user, because using "sh run.sh" then stops with these errors: ... galaxy.model.migrate.check DEBUG 2010-05-03 15:15:27,151 MySQL_python egg successfully loaded for mysql dialect 2010-05-03 15:15:27,187 INFO sqlalchemy.pool.QueuePool.0x...4f90 Error on connect(): (OperationalError) (1045, "Access denied for user 'bach'@'localhost' (using password: NO)") None None sqlalchemy.pool.QueuePool.0x...4f90 INFO 2010-05-03 15:15:27,187 Error on connect(): (OperationalError) (1045, "Access denied for user 'bach'@'localhost' (using password: NO)") None None Traceback (most recent call last): File "/bioinf/wwwservices/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) ... which is somewhat understandable as such user does not exist in the mysql database. I'm currently trying out Galaxy under my own account, in the end however it will run as separate user. 2) perhaps also important: should the mysql admin setup users, tables and other stuff in mysql? If so: which, how ... etc. Regards, Bastien PS: in case it's important: the hg clone is from "galaxy-dist", march 17. -- DSM Nutritional Products AG R&D Human Nutrition & Health Bioinformatics - Bldg. 203 / 115 P.O. Box 2676 CH-4002 Basel / Switzerland Tel. +41 61 815 8264 DISCLAIMER : This e-mail is for the intended recipient only If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.
Hi Bastien, You can specify a MySQL username and password in the MySQL URL, e.g. mysql://username:password@localhost:3306/galaxy?unix_socket=/var/run/mysqld/mysqld.sock Cheers, J. On May 3, 2010, at 9:56 AM, Chevreux, Bastien wrote:
Dear Galaxy devs,
I'd like to try a Galaxy installation with a database connection and have it use a freshly installed MySQL. It's a Kubuntu system where I just installed all needed packages, MySQL is up and running fine.
In the Galaxy "universe_wsgi.ini" I commented out the sqlite entry and activated the one for a DB connection and it now shows now this:
database_connection =mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock database_engine_option_echo = true database_engine_option_echo_pool = true database_engine_option_pool_size = 10 database_engine_option_max_overflow = 20 database_engine_option_pool_recycle = 7200
What I can't find in the online documents (Wiki) or via a Google search is:
1) how to tell Galaxy it should use a given MySQL user, because using "sh run.sh" then stops with these errors:
... galaxy.model.migrate.check DEBUG 2010-05-03 15:15:27,151 MySQL_python egg successfully loaded for mysql dialect 2010-05-03 15:15:27,187 INFO sqlalchemy.pool.QueuePool.0x...4f90 Error on connect(): (OperationalError) (1045, "Access denied for user 'bach'@'localhost' (using password: NO)") None None sqlalchemy.pool.QueuePool.0x...4f90 INFO 2010-05-03 15:15:27,187 Error on connect(): (OperationalError) (1045, "Access denied for user 'bach'@'localhost' (using password: NO)") None None Traceback (most recent call last): File "/bioinf/wwwservices/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) ...
which is somewhat understandable as such user does not exist in the mysql database. I'm currently trying out Galaxy under my own account, in the end however it will run as separate user.
2) perhaps also important: should the mysql admin setup users, tables and other stuff in mysql? If so: which, how ... etc.
Regards, Bastien
PS: in case it's important: the hg clone is from "galaxy-dist", march 17.
-- DSM Nutritional Products AG R&D Human Nutrition & Health Bioinformatics - Bldg. 203 / 115 P.O. Box 2676 CH-4002 Basel / Switzerland Tel. +41 61 815 8264
DISCLAIMER : This e-mail is for the intended recipient only If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.
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participants (2)
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Chevreux, Bastien -
Jeremy Goecks