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