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
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------------------------- 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