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
>
>