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

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

Sorry, did not see the localhost in there Now using: # instead. PostgreSQL and MySQL are supported. database_connection = mysql://xxx@xxx:localhost/galaxy?unix_socket=/var/lib/mysql/mysql.sock Still get the the issue with the post however: 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(): localhost On 3/9/10 8:46 AM, "Nate Coraor" <nate@bx.psu.edu> wrote: 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

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

Thanks... I have never used sqlalchemy so no knowledge on the connection string, now that I see it I could have come up with that myself though Works now Olaf On 3/9/10 9:09 AM, "Nate Coraor" <nate@bx.psu.edu> wrote: This is what happens when I go from memory. The DB engine URL documentation is here: http://www.sqlalchemy.org/docs/05/dbengine.html I had the '@' and ':' reversed. mysql://xxx:xxx@localhost/galaxy?unix_socket=/var/lib/mysql/mysql.sock Sorry for all the confusion. Stein, Olaf wrote:

Sorry, did not see the localhost in there Now using:

# instead. PostgreSQL and MySQL are supported. database_connection = mysql://xxx@xxx:localhost/galaxy?unix_socket=/var/lib/mysql/mysql.sock

Still get the the issue with the post however:

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(): localhost

On 3/9/10 8:46 AM, "Nate Coraor" <nate@bx.psu.edu> wrote:

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

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

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