Configuring MySQL for Galaxy (and vice versa) - galaxy-dev

3 May 2010


      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.
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