Dear Galaxy Dev Team,

We upgraded our Galaxy instance to the git repository from mercurial  old Galaxy-dist to Galaxy.  

When running the sh manage_db.sh -c ./config/galaxy.ini  upgrade   we get the following error.

Can you explain this error and more importantly how to correct the problem>

Thanks,

Bob

-bash-4.2$ sh manage_db.sh -c ./config/galaxy.ini upgrade
Traceback (most recent call last):
  File "./scripts/manage_db.py", line 33, in <module>
    invoke_migrate_main()
  File "./scripts/manage_db.py", line 30, in invoke_migrate_main
    main( repository=repo, url=db_url )
  File "/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/shell.py", line 209, in main
    ret = command_func(**kwargs)
  File "/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/api.py", line 186, in upgrade
    return _migrate(url, repository, version, upgrade=True, err=err, **opts)
  File "<string>", line 2, in _migrate
  File "/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/util/__init__.py", line 160, in with_engine
    return f(*a, **kw)
  File "/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/api.py", line 342, in _migrate
    schema = ControlledSchema(engine, repository)
  File "/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/schema.py", line 33, in __init__
    self.load()
  File "/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/schema.py", line 54, in load
    exceptions.DatabaseNotControlledError(str(exc)), tb)
  File "/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/schema.py", line 50, in load
    data = list(result)[0]
migrate.exceptions.DatabaseNotControlledError: list index out of range
-bash-4.2$