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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