I've upgraded my developmental Galaxy instance to the latest galaxy-dist release with a transplanted the drmaa.py patch from galaxy-central. All .conf files have been updated. However, I can't start the instance now The error listed below is generated. I tried enabling/disabling the toolshed configs, but that didn't resolve the issue. The database was upgraded from version 85 to 90 cleanly. Regards, Alex galaxy.datatypes.registry DEBUG 2012-02-07 12:32:12,345 Loaded converter: pbed2ldindepconvert galaxy.tools.imp_exp DEBUG 2012-02-07 12:32:12,360 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2012-02-07 12:32:12,367 Loaded history import tool: __IMPORT_HISTORY__ galaxy.datatypes.registry DEBUG 2012-02-07 12:32:12,383 Loaded external metadata tool: __SET_METADATA__ <Galaxy finished loading all tools> sqlalchemy.pool.QueuePool.0x...1290 WARNING 2012-02-07 12:32:12,831 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block Traceback (most recent call last): File "/galaxy/run/dev/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/galaxy/run/dev/lib/galaxy/app.py", line 83, in __init__ self.installed_repository_manager.load_proprietary_datatypes() File "/galaxy/run/dev/lib/galaxy/tool_shed/__init__.py", line 19, in load_proprietary_datatypes .order_by( self.model.ToolShedRepository.table.c.id ): File "/galaxy/run/dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ return self._execute_and_instances(context) File "/galaxy/run/dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File "/galaxy/run/dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/galaxy/run/dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/galaxy/run/dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/galaxy/run/dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File "/galaxy/run/dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File "/galaxy/run/dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) ProgrammingError: (ProgrammingError) column tool_shed_repository.uninstalled does not exist LINE 1: ...pository.deleted AS tool_shed_repository_deleted, tool_shed_... ^ 'SELECT tool_shed_repository.id AS tool_shed_repository_id, tool_shed_repository.create_time AS tool_shed_repository_create_time, tool_shed_repository.update_time AS tool_shed_repository_update_time, tool_shed_repository.tool_shed AS tool_shed_repository_tool_shed, tool_shed_repository.name AS tool_shed_repository_name, tool_shed_repository.description AS tool_shed_repository_description, tool_shed_repository.owner AS tool_shed_repository_owner, tool_shed_repository.installed_changeset_revision AS tool_shed_repository_installed_changeset_revision, tool_shed_repository.changeset_revision AS tool_shed_repository_changeset_revision, tool_shed_repository.metadata AS tool_shed_repository_metadata, tool_shed_repository.includes_datatypes AS tool_shed_repository_includes_datatypes, tool_shed_repository.update_available AS tool_shed_repository_update_available, tool_shed_repository.deleted AS tool_shed_repository_deleted, tool_shed_repository.uninstalled AS tool_shed_repository_uninstalled, tool_shed_repository.dist_to_shed AS tool_shed_repository_dist_to_shed \nFROM tool_shed_repository \nWHERE tool_shed_repository.includes_datatypes = %(includes_datatypes_1)s AND tool_shed_repository.deleted = %(deleted_1)s ORDER BY tool_shed_repository.id' {'includes_datatypes_1': True, 'deleted_1': False}