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 ========================================================