After a fresh galaxy-dist pull today (no update for various reasons) the 
instance was running ok on the default sqlight database.
When I migrated back the setting to use the MySQL database it complained during 
startup about having found an old version of the database and I need to upgrade.

Database upgrade started and the first few migrations were successful, but now 
it hangs every time at 99->100.

Any clue what might be wrong?

Here is the lengthy trace log.
thanks
Alex

====================================================
99 -> 100...

Migration script to alter the type of the tool_dependency.version column from 
TrimmedString(40) to Text.

Traceback (most recent call last):
  File "./scripts/manage_db.py", line 63, in <module>
    main( repository=repo, url=db_url )
  File 
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/shell.py",
 line 150, in main
    ret = command_func(**kwargs)
  File 
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py",
 line 221, in upgrade
    return _migrate(url, repository, version, upgrade=True, err=err, **opts)
  File 
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py",
 line 349, in _migrate
    schema.runchange(ver, change, changeset.step)
  File 
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py",
 line 184, in runchange
    change.run(self.engine, step)
  File 
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/script/py.py",
 line 101, in run
    func()
  File 
"lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py",
 line 30, in upgrade
    ToolDependency_table = Table( "tool_dependency", metadata, autoload=True )
  File 
"/opt/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 
"/opt/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 
"/opt/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 
"/opt/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 
"/opt/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)
sqlalchemy.exc.NoSuchTableError: tool_dependency
Error in sys.excepthook:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/apport_python_hook.py", line 66, in 
apport_excepthook
    from apport.fileutils import likely_packaged, get_recent_crashes
ImportError: No module named apport.fileutils

Original exception was:
Traceback (most recent call last):
  File "./scripts/manage_db.py", line 63, in <module>
    main( repository=repo, url=db_url )
  File 
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/shell.py",
 line 150, in main
    ret = command_func(**kwargs)
  File 
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py",
 line 221, in upgrade
    return _migrate(url, repository, version, upgrade=True, err=err, **opts)
  File 
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py",
 line 349, in _migrate
    schema.runchange(ver, change, changeset.step)
  File 
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py",
 line 184, in runchange
    change.run(self.engine, step)
  File 
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/script/py.py",
 line 101, in run
    func()
  File 
"lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py",
 line 30, in upgrade
    ToolDependency_table = Table( "tool_dependency", metadata, autoload=True )
  File 
"/opt/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 
"/opt/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 
"/opt/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 
"/opt/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 
"/opt/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)
sqlalchemy.exc.NoSuchTableError: tool_dependency
========================================================




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