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