- galaxy-dev - lists.galaxyproject.org

Error after migrating to latest changeset
by michael burrell (TSL) 17 Aug '11

17 Aug '11

Good Morning, I am getting a big problem with our production server when I upgrade to the latest change set (it was quite out of date). I have attached quite a long paster output to try and show whats going on, Our galaxy instance no longer seems to run jobs at all, they are not allocated a job runner and the following is given in the paster log I look forwards to your assistance. Thanks Michael. ====== galaxy.datatypes.registry DEBUG 2011-07-12 11:46:50,433 Loaded indexer: INDEXER_Interval_0 galaxy.jobs.runners.local INFO 2011-07-12 11:46:50,436 starting workers galaxy.jobs.runners.local DEBUG 2011-07-12 11:46:50,437 5 workers ready galaxy.jobs DEBUG 2011-07-12 11:46:50,438 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.runners.drmaa DEBUG 2011-07-12 11:46:50,483 10 workers ready galaxy.jobs DEBUG 2011-07-12 11:46:50,483 Loaded job runner: galaxy.jobs.runners.drmaa:DRMAAJobRunner galaxy.jobs INFO 2011-07-12 11:46:50,484 job manager started galaxy.jobs DEBUG 2011-07-12 11:46:50,861 no runner: 4400 is still in new state, adding to the jobs queue galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4401 is still in new state, adding to the jobs queue galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4403 is still in new state, adding to the jobs queue galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4404 is still in new state, adding to the jobs queue galaxy.jobs INFO 2011-07-12 11:46:50,869 job stopper started galaxy.sample_tracking.external_service_types DEBUG 2011-07-12 11:46:50,872 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2011-07-12 11:46:50,875 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,895 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,898 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,915 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,917 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,920 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,924 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,942 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,946 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,947 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,949 Enabling 'mobile' controller, class: Mobile galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,952 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,958 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,996 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,997 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,000 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,002 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,004 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,013 Enabling 'tracks' controller, class: TracksController galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,016 Enabling 'ucsc_proxy' controller, class: UCSCProxy galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,019 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,022 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,107 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,110 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,112 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,115 Enabling 'request_type' controller, class: RequestType galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,146 Enabling 'httpexceptions' middleware galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,148 Enabling 'recursive' middleware galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,169 Enabling 'error' middleware galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,173 Enabling 'trans logger' middleware galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,173 Enabling 'config' middleware galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,174 Enabling 'x-forwarded-host' middleware Starting server in PID 3738. serving on http://127.0.0.1:8080 sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:00,942 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block galaxy.jobs ERROR 2011-07-12 11:47:00,942 failure running job 4400 Traceback (most recent call last): File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 187, in __monitor_step job_state = self.__check_if_ready_to_run( job ) File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 232, in __check_if_ready_to_run for dataset_assoc in job.input_datasets + job.input_library_datasets: File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__ return self.impl.get(instance_state(instance), instance_dict(instance)) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get value = callable_() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__ result = q.all() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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) relation "job_to_input_library_dataset" does not exist 'SELECT job_to_input_library_dataset.id AS job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS job_to_input_library_dataset_job_id, job_to_input_library_dataset.ldda_id AS job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name AS job_to_input_library_dataset_name, library_dataset_dataset_association_1.id AS library_dataset_dataset_association_1_id, library_dataset_dataset_association_1.library_dataset_id AS library_dataset_dataset_association_1_library_dataset_id, library_dataset_dataset_association_1.dataset_id AS library_dataset_dataset_association_1_dataset_id, library_dataset_dataset_association_1.create_time AS library_dataset_dataset_association_1_create_time, library_dataset_dataset_association_1.update_time AS library_dataset_dataset_association_1_update_time, library_dataset_dataset_association_1.state AS library_dataset_dataset_association_1_state, library_dataset_dataset_association_1.copied_from_history_dataset_association_id AS library_dataset_dataset_association_1_copied_from_history_1, library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_1_copied_from_library_2, library_dataset_dataset_association_1.name AS library_dataset_dataset_association_1_name, library_dataset_dataset_association_1.info AS library_dataset_dataset_association_1_info, library_dataset_dataset_association_1.blurb AS library_dataset_dataset_association_1_blurb, library_dataset_dataset_association_1.peek AS library_dataset_dataset_association_1_peek, library_dataset_dataset_association_1.extension AS library_dataset_dataset_association_1_extension, library_dataset_dataset_association_1.metadata AS library_dataset_dataset_association_1_metadata, library_dataset_dataset_association_1.parent_id AS library_dataset_dataset_association_1_parent_id, library_dataset_dataset_association_1.designation AS library_dataset_dataset_association_1_designation, library_dataset_dataset_association_1.deleted AS library_dataset_dataset_association_1_deleted, library_dataset_dataset_association_1.visible AS library_dataset_dataset_association_1_visible, library_dataset_dataset_association_1.user_id AS library_dataset_dataset_association_1_user_id, library_dataset_dataset_association_1.message AS library_dataset_dataset_association_1_message \nFROM job_to_input_library_dataset LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_1 ON library_dataset_dataset_association_1.id = job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = job_to_input_library_dataset.job_id' {'param_1': 4400} sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:00,978 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block galaxy.jobs ERROR 2011-07-12 11:47:00,979 failure running job 4401 Traceback (most recent call last): File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 187, in __monitor_step job_state = self.__check_if_ready_to_run( job ) File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 232, in __check_if_ready_to_run for dataset_assoc in job.input_datasets + job.input_library_datasets: File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__ return self.impl.get(instance_state(instance), instance_dict(instance)) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get value = callable_() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__ result = q.all() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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) relation "job_to_input_library_dataset" does not exist 'SELECT job_to_input_library_dataset.id AS job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS job_to_input_library_dataset_job_id, job_to_input_library_dataset.ldda_id AS job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name AS job_to_input_library_dataset_name, library_dataset_dataset_association_1.id AS library_dataset_dataset_association_1_id, library_dataset_dataset_association_1.library_dataset_id AS library_dataset_dataset_association_1_library_dataset_id, library_dataset_dataset_association_1.dataset_id AS library_dataset_dataset_association_1_dataset_id, library_dataset_dataset_association_1.create_time AS library_dataset_dataset_association_1_create_time, library_dataset_dataset_association_1.update_time AS library_dataset_dataset_association_1_update_time, library_dataset_dataset_association_1.state AS library_dataset_dataset_association_1_state, library_dataset_dataset_association_1.copied_from_history_dataset_association_id AS library_dataset_dataset_association_1_copied_from_history_1, library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_1_copied_from_library_2, library_dataset_dataset_association_1.name AS library_dataset_dataset_association_1_name, library_dataset_dataset_association_1.info AS library_dataset_dataset_association_1_info, library_dataset_dataset_association_1.blurb AS library_dataset_dataset_association_1_blurb, library_dataset_dataset_association_1.peek AS library_dataset_dataset_association_1_peek, library_dataset_dataset_association_1.extension AS library_dataset_dataset_association_1_extension, library_dataset_dataset_association_1.metadata AS library_dataset_dataset_association_1_metadata, library_dataset_dataset_association_1.parent_id AS library_dataset_dataset_association_1_parent_id, library_dataset_dataset_association_1.designation AS library_dataset_dataset_association_1_designation, library_dataset_dataset_association_1.deleted AS library_dataset_dataset_association_1_deleted, library_dataset_dataset_association_1.visible AS library_dataset_dataset_association_1_visible, library_dataset_dataset_association_1.user_id AS library_dataset_dataset_association_1_user_id, library_dataset_dataset_association_1.message AS library_dataset_dataset_association_1_message \nFROM job_to_input_library_dataset LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_1 ON library_dataset_dataset_association_1.id = job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = job_to_input_library_dataset.job_id' {'param_1': 4401} sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:00,999 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block galaxy.jobs ERROR 2011-07-12 11:47:00,999 failure running job 4403 Traceback (most recent call last): File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 187, in __monitor_step job_state = self.__check_if_ready_to_run( job ) File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 232, in __check_if_ready_to_run for dataset_assoc in job.input_datasets + job.input_library_datasets: File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__ return self.impl.get(instance_state(instance), instance_dict(instance)) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get value = callable_() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__ result = q.all() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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) relation "job_to_input_library_dataset" does not exist 'SELECT job_to_input_library_dataset.id AS job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS job_to_input_library_dataset_job_id, job_to_input_library_dataset.ldda_id AS job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name AS job_to_input_library_dataset_name, library_dataset_dataset_association_1.id AS library_dataset_dataset_association_1_id, library_dataset_dataset_association_1.library_dataset_id AS library_dataset_dataset_association_1_library_dataset_id, library_dataset_dataset_association_1.dataset_id AS library_dataset_dataset_association_1_dataset_id, library_dataset_dataset_association_1.create_time AS library_dataset_dataset_association_1_create_time, library_dataset_dataset_association_1.update_time AS library_dataset_dataset_association_1_update_time, library_dataset_dataset_association_1.state AS library_dataset_dataset_association_1_state, library_dataset_dataset_association_1.copied_from_history_dataset_association_id AS library_dataset_dataset_association_1_copied_from_history_1, library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_1_copied_from_library_2, library_dataset_dataset_association_1.name AS library_dataset_dataset_association_1_name, library_dataset_dataset_association_1.info AS library_dataset_dataset_association_1_info, library_dataset_dataset_association_1.blurb AS library_dataset_dataset_association_1_blurb, library_dataset_dataset_association_1.peek AS library_dataset_dataset_association_1_peek, library_dataset_dataset_association_1.extension AS library_dataset_dataset_association_1_extension, library_dataset_dataset_association_1.metadata AS library_dataset_dataset_association_1_metadata, library_dataset_dataset_association_1.parent_id AS library_dataset_dataset_association_1_parent_id, library_dataset_dataset_association_1.designation AS library_dataset_dataset_association_1_designation, library_dataset_dataset_association_1.deleted AS library_dataset_dataset_association_1_deleted, library_dataset_dataset_association_1.visible AS library_dataset_dataset_association_1_visible, library_dataset_dataset_association_1.user_id AS library_dataset_dataset_association_1_user_id, library_dataset_dataset_association_1.message AS library_dataset_dataset_association_1_message \nFROM job_to_input_library_dataset LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_1 ON library_dataset_dataset_association_1.id = job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = job_to_input_library_dataset.job_id' {'param_1': 4403} sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:01,027 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block galaxy.jobs ERROR 2011-07-12 11:47:01,028 failure running job 4404 Traceback (most recent call last): File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 187, in __monitor_step job_state = self.__check_if_ready_to_run( job ) File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 232, in __check_if_ready_to_run for dataset_assoc in job.input_datasets + job.input_library_datasets: File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__ return self.impl.get(instance_state(instance), instance_dict(instance)) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get value = callable_() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__ result = q.all() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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) relation "job_to_input_library_dataset" does not exist 'SELECT job_to_input_library_dataset.id AS job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS job_to_input_library_dataset_job_id, job_to_input_library_dataset.ldda_id AS job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name AS job_to_input_library_dataset_name, library_dataset_dataset_association_1.id AS library_dataset_dataset_association_1_id, library_dataset_dataset_association_1.library_dataset_id AS library_dataset_dataset_association_1_library_dataset_id, library_dataset_dataset_association_1.dataset_id AS library_dataset_dataset_association_1_dataset_id, library_dataset_dataset_association_1.create_time AS library_dataset_dataset_association_1_create_time, library_dataset_dataset_association_1.update_time AS library_dataset_dataset_association_1_update_time, library_dataset_dataset_association_1.state AS library_dataset_dataset_association_1_state, library_dataset_dataset_association_1.copied_from_history_dataset_association_id AS library_dataset_dataset_association_1_copied_from_history_1, library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_1_copied_from_library_2, library_dataset_dataset_association_1.name AS library_dataset_dataset_association_1_name, library_dataset_dataset_association_1.info AS library_dataset_dataset_association_1_info, library_dataset_dataset_association_1.blurb AS library_dataset_dataset_association_1_blurb, library_dataset_dataset_association_1.peek AS library_dataset_dataset_association_1_peek, library_dataset_dataset_association_1.extension AS library_dataset_dataset_association_1_extension, library_dataset_dataset_association_1.metadata AS library_dataset_dataset_association_1_metadata, library_dataset_dataset_association_1.parent_id AS library_dataset_dataset_association_1_parent_id, library_dataset_dataset_association_1.designation AS library_dataset_dataset_association_1_designation, library_dataset_dataset_association_1.deleted AS library_dataset_dataset_association_1_deleted, library_dataset_dataset_association_1.visible AS library_dataset_dataset_association_1_visible, library_dataset_dataset_association_1.user_id AS library_dataset_dataset_association_1_user_id, library_dataset_dataset_association_1.message AS library_dataset_dataset_association_1_message \nFROM job_to_input_library_dataset LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_1 ON library_dataset_dataset_association_1.id = job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = job_to_input_library_dataset.job_id' {'param_1': 4404} 149.155.218.28 - - [12/Jul/2011:11:47:31 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_8; en-us) AppleWebKit/533.21.1 (KHTML, like Gecko) Version/5.0.5 Safari/533.21.1" 149.155.221.116 - - [12/Jul/2011:11:47:33 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-GB; rv:1.9.2.19) Gecko/20110707 Firefox/3.6.19" 149.155.221.194 - - [12/Jul/2011:11:47:33 +0100] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" 149.155.221.194 - - [12/Jul/2011:11:47:33 +0100] "GET /history HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" 149.155.221.194 - - [12/Jul/2011:11:47:33 +0100] "GET /root/tool_menu HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" 149.155.218.28 - - [12/Jul/2011:11:47:35 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_8; en-us) AppleWebKit/533.21.1 (KHTML, like Gecko) Version/5.0.5 Safari/533.21.1" 149.155.221.116 - - [12/Jul/2011:11:47:37 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-GB; rv:1.9.2.19) Gecko/20110707 Firefox/3.6.19" 149.155.221.194 - - [12/Jul/2011:11:47:36 +0100] "GET /tool_runner/rerun?id=6014 HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" 149.155.221.194 - - [12/Jul/2011:11:47:38 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" 149.155.218.28 - - [12/Jul/2011:11:47:39 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_8; en-us) AppleWebKit/533.21.1 (KHTML, like Gecko) Version/5.0.5 Safari/533.21.1" 149.155.221.194 - - [12/Jul/2011:11:47:39 +0100] "POST /tool_runner/index HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/tool_runner/rerun?id=6014" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:40,371 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block galaxy.jobs ERROR 2011-07-12 11:47:40,372 failure running job 4405 Traceback (most recent call last): File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 187, in __monitor_step job_state = self.__check_if_ready_to_run( job ) File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 232, in __check_if_ready_to_run for dataset_assoc in job.input_datasets + job.input_library_datasets: File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__ return self.impl.get(instance_state(instance), instance_dict(instance)) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get value = callable_() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__ result = q.all() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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 "/home/home/galaxy/software/galaxy-ceneral/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) relation "job_to_input_library_dataset" does not exist 'SELECT job_to_input_library_dataset.id AS job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS job_to_input_library_dataset_job_id, job_to_input_library_dataset.ldda_id AS job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name AS job_to_input_library_dataset_name, library_dataset_dataset_association_1.id AS library_dataset_dataset_association_1_id, library_dataset_dataset_association_1.library_dataset_id AS library_dataset_dataset_association_1_library_dataset_id, library_dataset_dataset_association_1.dataset_id AS library_dataset_dataset_association_1_dataset_id, library_dataset_dataset_association_1.create_time AS library_dataset_dataset_association_1_create_time, library_dataset_dataset_association_1.update_time AS library_dataset_dataset_association_1_update_time, library_dataset_dataset_association_1.state AS library_dataset_dataset_association_1_state, library_dataset_dataset_association_1.copied_from_history_dataset_association_id AS library_dataset_dataset_association_1_copied_from_history_1, library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_1_copied_from_library_2, library_dataset_dataset_association_1.name AS library_dataset_dataset_association_1_name, library_dataset_dataset_association_1.info AS library_dataset_dataset_association_1_info, library_dataset_dataset_association_1.blurb AS library_dataset_dataset_association_1_blurb, library_dataset_dataset_association_1.peek AS library_dataset_dataset_association_1_peek, library_dataset_dataset_association_1.extension AS library_dataset_dataset_association_1_extension, library_dataset_dataset_association_1.metadata AS library_dataset_dataset_association_1_metadata, library_dataset_dataset_association_1.parent_id AS library_dataset_dataset_association_1_parent_id, library_dataset_dataset_association_1.designation AS library_dataset_dataset_association_1_designation, library_dataset_dataset_association_1.deleted AS library_dataset_dataset_association_1_deleted, library_dataset_dataset_association_1.visible AS library_dataset_dataset_association_1_visible, library_dataset_dataset_association_1.user_id AS library_dataset_dataset_association_1_user_id, library_dataset_dataset_association_1.message AS library_dataset_dataset_association_1_message \nFROM job_to_input_library_dataset LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_1 ON library_dataset_dataset_association_1.id = job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = job_to_input_library_dataset.job_id' {'param_1': 4405} 149.155.221.194 - - [12/Jul/2011:11:47:40 +0100] "GET /user/get_most_recently_used_tool_async HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/root/tool_menu" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" 149.155.221.194 - - [12/Jul/2011:11:47:40 +0100] "GET /history HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/tool_runner/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" 149.155.221.116 - - [12/Jul/2011:11:47:41 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-GB; rv:1.9.2.19) Gecko/20110707 Firefox/3.6.19" 149.155.221.194 - - [12/Jul/2011:11:47:42 +0100] "GET /root/delete_async?id=6014 HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" 149.155.218.28 - - [12/Jul/2011:11:47:43 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_8; en-us) AppleWebKit/533.21.1 (KHTML, like Gecko) Version/5.0.5 Safari/533.21.1"

2 1

Data library fails to display contents
by W. Augustine Dunn III 17 Aug '11

17 Aug '11

I am starting to really get the hang of customizing my new galaxy instance, and please just let me THANK YOU GUYS! However, I am also running into a problem. I am trying to link genome fasta files that i obtained through metazoa.ensembl.org. I created a library called "Genome Sequences" with sub-folders to house them. Everything was going fine until I tried to change the info on a couple so that they were fasta not so other randomly autoassigned type. Now I get this error msg when ever i try to browse ANY of the "Genome Seq" Library: Error attempting to display contents of library (Genome Sequences): 'NoneType' object has no attribute 'dataset'. I am running this instance using a postgresql backend but the default paste web-server since its mostly gonna me me and one or two other lab-mates using it. I can NOT figure out whats up. Relevant excerpt of Server log follows: xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:03 -0700] "GET / HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/library" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:04 -0700] "GET /root/tool_menu HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:04 -0700] "GET /history HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:07 -0700] "GET /admin HTTP/1.1" 200 - "http://vlad.bio.uci.edu:8081/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:07 -0700] "GET /admin/center?webapp=galaxy HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/admin" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:10 -0700] "GET /library_admin/browse_libraries HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/admin" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:12 -0700] "GET /library_admin/browse_libraries?f-deleted=False&f-name=All&f-description=All&sort=name&show_item_checkboxes=false&async=false&page=1&webapp=galaxy&operation=browse&id=9a8774fee61dd122& HTTP/1.1" 302 - "http://xxx.xxx.xxx.xxx/library_admin/browse_libraries" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:12 -0700] "GET /library_common/browse_library?sort=name&operation=browse&f-description=All&f-name=All&f-deleted=False&cntrller=library_admin&async=false&show_item_checkboxes=false&webapp=galaxy&id=9a8774fee61dd122&page=1 HTTP/1.1" 302 - "http://xxx.xxx.xxx.xxx/library_admin/browse_libraries" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:12 -0700] "GET /library_admin/browse_libraries?status=error&use_panels=False&message=Error+attempting+to+display+contents+of+library+%28Genome+Sequences%29%3A+__sq__NoneType__sq__+object+has+no+attribute+__sq__dataset__sq__. HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/library_admin/browse_libraries" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" Thanks in advance! And thanks for this priceless tool! Gus -- In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. *-Stephen Jay Gould*

2 1

Re: [galaxy-dev] Parallel job through galaxy
by Peter Cock 16 Aug '11

16 Aug '11

On Tue, Aug 16, 2011 at 11:13 AM, shashi shekhar <meshashi29(a)gmail.com> wrote: > Thanks Peter for reply > But i want to use galaxy for parallel programs like mpi and opemp .will it > support ?how can i configure for parallel programs ? Please CC the mailing list. Tools using openmp should be easy. MPI is more complicated. First check you can submit test MPI jobs to PBS by hand, then setup the job runner in Galaxy to use the same settings. Peter

2 1

Parallel job through galaxy
by shashi shekhar 16 Aug '11

16 Aug '11

Hi All, I have local instance of Galaxy .I have system of very good configuration .it has many cores and I want to use multiprocessor for some tool. Have you added any tool which uses multiprocessor in Galaxy ? Provide me tool name . in my system pbs is installed . How can i use multiprocessor in Galaxy ? Regards shashi shekhar

2 1

Defining new file formats in Galaxy (for new tool wrappers)
by Peter Cock 16 Aug '11

16 Aug '11

Hi all, Something I've not needed to do until now is define a new file format in Galaxy. I understand the basic principle and defining a subclass in Python... however, how does this work with new tools on the Tool Shed? In particular, if an output format is likely to be used by more than one tool, can we get it added to the Galaxy core? As an example, the basic functionality of the Blast2GO for pipelines tool (b2g4pipe) takes a BLAST XML input file, and gives a tab separated annotation output file. Galaxy already has 'blastxml' and 'tabular' file formats defined, so I didn't need to do anything extra. However, the tool can also take (a directory of) InterProScan XML files as input, so here a new 'interproscanxml' format would useful. Then any wrapper using or producing InterProScan XML could take advantage of this. e.g. Konrad's InterProScan wrapper could then offer the XML output as an option in addition to or instead of the tabular output. Related to this example, why isn't there a generic base class for XML formats in general? https://bitbucket.org/galaxy/galaxy-central/issue/568/missing-xml-datatype-… Regards, Peter

3 12

Re: [galaxy-dev] [galaxy-user] uploading files via FTP
by Nate Coraor 16 Aug '11

16 Aug '11

somy ork wrote: > Hi Nate, > > Thanks for you reply. > I am using windows7 and i use cygwin-X to access my server which has galaxy > installed in it. > I have filezilla installed on my windows pc. Now the problem is, in the > upload option, I could > only the see the file upload and url upload options on my galaxy page. > Why am i not able to see the FTP upload option? > Is there any settings which i need to change in the galaxy configuration?? > Since i am a non-technical person, i kindly request you to help me solve > this problem. > https://bitbucket.org/galaxy/galaxy-central/wiki/Config/UploadViaFTP this > webpage didnt solve my problem as well. The section under "Configuring Galaxy" is the only relevant part for your setup. Simply set, in universe_wsgi.ini: ftp_upload_dir = /path/to/ftp_directory ftp_upload_site = Name of server to connect to via SFTP. Then restart Galaxy. --nate > > Thank you once again. > Regards > Somy. > > > On Mon, Jun 13, 2011 at 10:57 PM, Nate Coraor <nate(a)bx.psu.edu> wrote: > > > somy ork wrote: > > > Hi, > > > > > > Am trying to configure galaxy to enable file upload via FTP. > > > My server is configured with SFTP. and not FTP. > > > Will this create a problem in galaxy? coz all my input files are above 2 > > GB. > > > Should i change any settings in the universe_wsgi.ini file? > > > Please guide me. > > > > Hi Somy, > > > > SFTP is fine for your local site, I really need to just generalize those > > configuration options and the wording so that is not specific to FTP. > > The same code can actually just be used to provide access to local > > directories that users can copy data into via whatever means is most > > appropriate for their own site. > > > > --nate > > > > > > > > Regards > > > somy. > > > > > ___________________________________________________________ > > > The Galaxy User list should be used for the discussion of > > > Galaxy analysis and other features on the public server > > > at usegalaxy.org. Please keep all replies on the list by > > > using "reply all" in your mail client. For discussion of > > > local Galaxy instances and the Galaxy source code, please > > > use the Galaxy Development list: > > > > > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > > > > > To manage your subscriptions to this and other Galaxy lists, > > > please use the interface at: > > > > > > http://lists.bx.psu.edu/ > > > >

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Re: [galaxy-dev] suggestion for multithreading
by Andrew Warren 16 Aug '11

16 Aug '11

So would the current correct method for setting up multi-threaded jobs on a cluster be to specify custom runners in the [galaxy:tool_runners] section of the universe config file for EVERY tool that uses a multiple threads (assuming the default is set to one)? For example, for the bowtie program and a queue named "galaxy": *bowtie = pbs:///galaxy/-l ppn=4,mem=16gb/* * * Is this currently the only way for galaxy to inform the queuing system how many threads a program will use? And does this mean that without custom runners in the config file any muti-threaded program that has multiple instances in an asychronous workflow has the opportunity to overload a cluster node since the queuing system doesn't "know" how many threads the program will be using? Just want to make sure I'm not missing out on the latest and greatest method for process management. :) Thanks, Andrew * * Louise-Amélie Schmitt wrote: > > > > default_cluster_job_runner will remain for backwards compatibility, but > > we'll ship a sample job_conf.xml that runs everything locally by > > default. > > > > --nate > > Haha, and I did that before realizing I could do just what I needed by > writing tool-specific *pbs*:// URLs at the end of the config file... I'm such > an idiot. Haha, okay, I don't think i even noticed since I was distracted by your implementation being a step in the way we want to go with it. > But I really like what you did of it and I have a couple of questions. > > Concerning the single-threaded tools, what would happen if the number of > threads set in the xml file was >1 ? It'd consume extra slots, but the tool itself would just run as usual. > Could it be possible to forbid a tool to run on a given node? Hrm. In *PBS* you could do it using node properties/neednodes or resource requirements. I'd have to think a bit about how to do this in a more general way in the XML. --nate > > Thanks, > L-A > > > > > >> > >> Peter > >>

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Re: [galaxy-dev] Adding Link to Sequencing Requests Page
by Greg Von Kuster 15 Aug '11

15 Aug '11

Hello Joe, Galaxy uses a combination of Python and mako templates for rendering - see http://www.makotemplates.org/ for information about mako templates. Assuming the "Sequencing Requests" page to which you refer looks something like the following, you'll need to modify the Python code in the RequestsGrid class in ~/lib/galaxy/web/controllers/requests_common.py. Good luck, and thanks for using Galaxy, Greg Von Kuster Sequencing Requests Create new request Advanced Search Name Description Samples Type Last Updated ↑ State No Items For 0 selected items: > Submitted by jcruz7(a)gmail.com > Hello Everyone, > > I would like to add a link to the Sequencing Requests page and modify it > further in the future but I'm unsure of how to go about doing that, since > there is no static html file for the webpage (at least none that I can find) > and I'm a newbie when it comes to web application development. > > I appreciate your help and patience. > > joe

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global configuration of email "from" possible?
by Holger Klein 15 Aug '11

15 Aug '11

Hi all, for the email functionality of our local galaxy instance I'm forced to use SMTP authentication and to use a specific "from", which is different to what galaxy generates automatically. Now galaxy generates a "from" like galaxy(a)computeserver.imb.uni-mainz.de but I want to set this to galaxy(a)imb-mainz.de. A quick check shows that the send_mail function defined in lib/galaxy/util/__init__.py is called in various places. Is there a way to set the "from" to a specific value? If not, it send_mail the only galaxy-function used to send mail? Cheers, Holger -- Dr. Holger Klein Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de/ Tel: +49(6131) 39 21511

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Whole genome simulation with dwgsim
by Nils Homer 15 Aug '11

15 Aug '11

I wanted to plug two tools that we have wrapped up for Galaxy: whole genome simulation of NGS reads, as well as the evaluation of the resulting mappings of those reads. This could be very useful for those that want to evaluate mapping algorithms, or experiment with simulated NGS data. Check out the "dwgsim" and "dwgsim_eval" tools at http://toolshed.g2.bx.psu.edu/ The tools and wrapper code can also be found at http://dnaa.sf.net, and described at https://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Whole_Genome_Si… Feedback and comments are very welcome, Nils Homer

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