Alex,

I've created the following ticket for this issue as it looks to be a bug with 
Galaxy / mysql.  You can follow the ticket to be aware of progress.

https://bitbucket.org/galaxy/galaxy-central/issue/660/galaxy-installation-with-mysql-database

Thanks for reporting this,

Greg Von Kuster


On Sep 14, 2011, at 7:35 PM, Alex R Bigelow wrote:

> Hi,
> I am trying to install a local instance of Galaxy with an infobright mysql 
> server; I created a database called "galaxy" (the user is also "galaxy," and 
> it has all the privileges it should need), and the database_connection line 
> is as follows:
> 
> database_connection = 
> mysql://galaxy:***********@localhost/galaxy?unix_socket=/tmp/mysql-ib.sock
> 
> When I do this, I get the following error:
> Traceback (most recent call last):
>  File "/gen21/alex/Apps/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in 
> app_factory
>    app = UniverseApplication( global_conf = global_conf, **kwargs )
>  File "/gen21/alex/Apps/galaxy-dist/lib/galaxy/app.py", line 32, in __init__
>    create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( 
> '__file__', None ), self.config.database_engine_options )
>  File "/gen21/alex/Apps/galaxy-dist/lib/galaxy/model/migrate/check.py", line 
> 65, in create_or_verify_database
>    db_schema = schema.ControlledSchema( engine, migrate_repository )
>  File 
> "/gen21/alex/Apps/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py",
>  line 24, in __init__
>    self._load()
>  File 
> "/gen21/alex/Apps/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py",
>  line 36, in _load
>    self.table = Table(tname, self.meta, autoload=True)
>  File 
> "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py",
>  line 108, in __call__
>    return type.__call__(self, name, metadata, *args, **kwargs)
>  File 
> "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py",
>  line 236, in __init__
>    _bind_or_error(metadata).reflecttable(self, 
> include_columns=include_columns)
>  File 
> "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py",
>  line 1265, in reflecttable
>    self.dialect.reflecttable(conn, table, include_columns)
>  File 
> "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/databases/mysql.py",
>  line 1664, in reflecttable
>    sql = self._show_create_table(connection, table, charset)
>  File 
> "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/databases/mysql.py",
>  line 1835, in _show_create_table
>    raise exc.NoSuchTableError(full_name)
> NoSuchTableError: migrate_version
> 
> I found this question in the archives:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-March/002216.html
> 
> As per both replies, I tried a virtual_env, which didn't work, and I also 
> deleted the "galaxy" database so that it would create a fresh one, but, of 
> course, now it can't connect to the database because it doesn't exist. How do 
> I tell Galaxy to create the database it needs?
> 
> Thanks again for all the support,
> Alex Bigelow
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu




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