Ah, probably the :, I thought it was valid to leave out the hostname
when connecting via a socket.  Try:

mysql://xxx@xxx:localhost/galaxy?unix_socket=/var/lib/mysql/mysql.sock

Stein, Olaf wrote:
> database_connection =
> mysql://xxx@xxx:/galaxy?unix_socket=/var/lib/mysql/mysql.sock
>
>
>
> On 3/8/10 10:13 PM, "Kanwei Li" <kanwei@gmail.com> wrote:
>
>     Hi Olaf,
>
>     Could you paste the DB url you're using? Anonymizing the user/pass
>     of course.
>
>     Thanks,
>
>     Kanwei
>
>     On Mon, Mar 8, 2010 at 4:08 PM, Stein, Olaf
>     <Olaf.Stein@nationwidechildrens.org> wrote:
>     >  Thanks
>     >
>     >  Now I get this:
>     >
>     >  galaxy.model.migrate.check DEBUG 2010-03-08 14:04:00,428
>     MySQL_python egg
>     >  successfully loaded for mysql dialect
>     >  Traceback (most recent call last):
>     >    File
>     "/export/home/steino/galaxy-dist/lib/galaxy/web/buildapp.py", line
>     >  61, in app_factory
>     >      app = UniverseApplication( global_conf = global_conf, **kwargs )
>     >    File "/export/home/steino/galaxy-dist/lib/galaxy/app.py", line
>     28, in
>     >  __init__
>     >      create_or_verify_database( db_url,
>     self.config.database_engine_options )
>     >    File
>     "/export/home/steino/galaxy-dist/lib/galaxy/model/migrate/check.py",
>     >  line 50, in create_or_verify_database
>     >      engine = create_engine( url, **engine_options )
>     >    File
>     >
>     "/export/home/steino/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/__init__.py",
>     >  line 223, in create_engine
>     >      return strategy.create(*args, **kwargs)
>     >    File
>     >
>     "/export/home/steino/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/strategies.py",
>     >  line 46, in create
>     >      u = url.make_url(name_or_url)
>     >    File
>     >
>     "/export/home/steino/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/url.py",
>     >  line 137, in make_url
>     >      return _parse_rfc1738_args(name_or_url)
>     >    File
>     >
>     "/export/home/steino/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/url.py",
>     >  line 173, in _parse_rfc1738_args
>     >      return URL(name, **components)
>     >    File
>     >
>     "/export/home/steino/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/url.py",
>     >  line 49, in __init__
>     >      self.port = int(port)
>     >  ValueError: invalid literal for int():
>     >
>     >
>     >
>     >  And my mysql port is standard 3306.
>     >
>     >  Any ideas?
>     >
>     >  Thanks
>     >  Olaf
>     >
>     >
>     >  On 3/8/10 1:51 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
>     >
>     >  Stein, Olaf wrote:
>     > > Hi all,
>     > >
>     > > Very new to galaxy and trying to setup an instance here with mysql as
>     > > the backend database.
>     > >
>     > > I added this line:
>     > > mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock
>     > >
>     > > To the universe_wsgi.ini file
>     > > Where do I define the dbuser, password and database that I want
>     to use?
>     > > And what else do I need to do, for instance create the schema, etc?
>     >
>     >  Hi Olaf,
>     >
>     >  Galaxy will automatically create the tables/etc. upon startup.  To set
>     >  the user, password, and database, use a URL like this:
>     >
>     >  mysql://user@pass:/dbname?unix_socket=/var/run/mysqld/mysqld.sock
>     >
>     >  --nate
>     >
>     > >
>     > > Thanks
>     > > Olaf
>     > >
>     > >
>     > >
>     > >
>     > >
>     > > -------------------------
>     > > Olaf Stein
>     > > DBA
>     > > Battelle Center for Mathematical Medicine
>     > > Nationwide Children's Hospital, The Research Institute
>     > > 700 Children's Drive
>     > > 43205 Columbus, OH
>     > > phone: 1-614-355-5685
>     > > cell: 1-614-843-0432
>     > > email: olaf.stein@nationwidechildrens.org
>     > >
>     > >
>     > > “I consider that the golden rule requires that if I like a program I
>     > > must share it with other people who like it.”
>     > > Richard M. Stallman
>     > >
>     > >
>     > >
>     ------------------------------------------------------------------------
>     > >
>     > > _______________________________________________
>     > > galaxy-user mailing list
>     > > galaxy-user@lists.bx.psu.edu
>     > > http://lists.bx.psu.edu/listinfo/galaxy-user
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >  -------------------------
>     >  Olaf Stein
>     >  DBA
>     >  Battelle Center for Mathematical Medicine
>     >  Nationwide Children's Hospital, The Research Institute
>     >  700 Children's Drive
>     >  43205 Columbus, OH
>     >  phone: 1-614-355-5685
>     >  cell: 1-614-843-0432
>     >  email: olaf.stein@nationwidechildrens.org
>     >
>     >
>     >  “I consider that the golden rule requires that if I like a program
>     I must
>     >  share it with other people who like it.”
>     >  Richard M. Stallman
>     >
>     >  _______________________________________________
>     >  galaxy-user mailing list
>     >  galaxy-user@lists.bx.psu.edu
>     >  http://lists.bx.psu.edu/listinfo/galaxy-user
>     >
>     >
>
>
>
>
>
>
> -------------------------
> Olaf Stein
> DBA
> Battelle Center for Mathematical Medicine
> Nationwide Children's Hospital, The Research Institute
> 700 Children's Drive
> 43205 Columbus, OH
> phone: 1-614-355-5685
> cell: 1-614-843-0432
> email: olaf.stein@nationwidechildrens.org
>
>
> “I consider that the golden rule requires that if I like a program I
> must share it with other people who like it.”
> Richard M. Stallman