Hi,
I'm running into issues with our galaxy installation regarding the new_file_path setting:
1/ clean up : ======== Can I safely delete all contents in the tmp folder using a cronjob, or manually when galaxy is (not) running. I have gathered almost 700Gb and
72K files on data there apparently. I suppose they are remnants of
crashed jobs
2/ Should it be accessible by all nodes ======================= Since I have that much data there, I suppose it does. However, it would make sense to use a seperate (local /tmp/ ?) folder for toolshed actions such as installations. As an example, I tried to install the package_perl from the test toolshed. On our production server, hosting the new_file_path on a NFS share with the 700GB / 72K files, this process ran for over 24 hours, then crashed the main process with the error below. On my development box (laptop, no network drives, single galaxy process), the package installed in under five minutes.
Best,
Geert
==========
tool_shed.galaxy_install.install_manager ERROR 2014-08-01 05:10:20,656 Error installing tool dependency perl version 5.18.1. Traceback (most recent call last): File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 110, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( app, tool_shed_repository, tool_dependency, actions_dict ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 94, in install_and_build_package initial_download=False ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step initial_download=initial_download ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 510, in execute_step return_output=False ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 148, in handle_command context.flush() File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush self._flush(objects) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1807, in _flush transaction.rollback(_capture_exception=True) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 386, in rollback transaction._rollback_impl() File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 414, in _rollback_impl t[1].rollback() File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2034, in rollback self._do_rollback() File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2071, in _do_rollback self.connection._rollback_impl() File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1265, in _rollback_impl self._handle_dbapi_exception(e, None, None, None, None) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1262, in _rollback_impl self.engine.dialect.do_rollback(self.connection) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 1910, in do_rollback connection.rollback() OperationalError: (OperationalError) (2006, 'MySQL server has gone away') None None tool_shed.util.common_install_util ERROR 2014-08-01 05:10:20,743 Error installing tool dependency perl version 5.18.1: Can't reconnect until invalid transaction is rolled back (original cause: InvalidRequestError: Can't reconnect until invalid transaction is rolled back) 'UPDATE tool_dependency SET update_time=%s, status=%s, error_message=%s WHERE tool_dependency.id = %s' [{'status': 'Error', 'error_message': ' File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 110, in install_and_build_package_via_fabric\n tool_dependency = self.install_and_build_package( app, tool_shed_repository, tool_dependency, actions_dict )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 94, in install_and_build_package\n initial_download=False )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step\n initial_download=initial_download )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 510, in execute_step\n return_output=False )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 148, in handle_command\n context.flush()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do\n return getattr(self.registry(), name)(*args, **kwargs)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush\n self._flush(objects)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1807, in _flush\n transaction.rollback(_capture_exception=True)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 386, in rollback\n transaction._rollback_impl()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 414, in _rollback_impl\n t[1].rollback()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2034, in rollback\n self._do_rollback()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2071, in _do_rollback\n self.connection._rollback_impl()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1265, in _rollback_impl\n self._handle_dbapi_exception(e, None, None, None, None)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1262, in _rollback_impl\n self.engine.dialect.do_rollback(self.connection)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 1910, in do_rollback\n connection.rollback()\n\n(OperationalError) (2006, 'MySQL server has gone away') None None', u'tool_dependency_id': 326L}] Traceback (most recent call last): File "/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py", line 554, in install_specified_tool_dependencies from_tool_migration_manager=from_tool_migration_manager ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 313, in install_package action_elem=None ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 176, in install_via_fabric tool_dependency = self.install_and_build_package_via_fabric( app, tool_shed_repository, tool_dependency, actions_dict ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 119, in install_and_build_package_via_fabric remove_installation_path=False ) File "/galaxy/galaxy-dist/lib/tool_shed/util/tool_dependency_util.py", line 423, in handle_tool_dependency_installation_error sa_session.flush() File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush self._flush(objects) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1789, in _flush flush_context.execute() File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py", line 331, in execute rec.execute(self) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py", line 475, in execute uow File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", line 59, in save_obj mapper, table, update) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", line 485, in _emit_update_statements execute(statement, params) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1449, in execute params) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1584, in _execute_clauseelement compiled_sql, distilled_params File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1651, in _execute_context None, None) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1645, in _execute_context conn = self._revalidate_connection() File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1044, in _revalidate_connection "Can't reconnect until invalid " StatementError: Can't reconnect until invalid transaction is rolled back (original cause: InvalidRequestError: Can't reconnect until invalid transaction is rolled back) 'UPDATE tool_dependency SET update_time=%s, status=%s, error_message=%s WHERE tool_dependency.id = %s' [{'status': 'Error', 'error_message': ' File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 110, in install_and_build_package_via_fabric\n tool_dependency = self.install_and_build_package( app, tool_shed_repository, tool_dependency, actions_dict )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 94, in install_and_build_package\n initial_download=False )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step\n initial_download=initial_download )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 510, in execute_step\n return_output=False )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 148, in handle_command\n context.flush()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do\n return getattr(self.registry(), name)(*args, **kwargs)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush\n self._flush(objects)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1807, in _flush\n transaction.rollback(_capture_exception=True)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 386, in rollback\n transaction._rollback_impl()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 414, in _rollback_impl\n t[1].rollback()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2034, in rollback\n self._do_rollback()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2071, in _do_rollback\n self.connection._rollback_impl()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1265, in _rollback_impl\n self._handle_dbapi_exception(e, None, None, None, None)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1262, in _rollback_impl\n self.engine.dialect.do_rollback(self.connection)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 1910, in do_rollback\n connection.rollback()\n\n(OperationalError) (2006, 'MySQL server has gone away') None None', u'tool_dependency_id': 326L}] 143.169.236.220 - - [31/Jul/2014:14:54:50 +0200] "POST /galaxy/admin_toolshed/manage_repositories HTTP/1.1" 500 - "http://biominavm-galaxy.biomina.be/galaxy/admin_toolshed/prepare_for_install" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/34.0.1847.116 Chrome/34.0.1847.116 Safari/537.36" Error - <class 'sqlalchemy.exc.InvalidRequestError'>: This Session's transaction has been rolled back due to a previous exception during flush. To begin a new transaction with this Session, first issue Session.rollback(). Original exception was: Can't reconnect until invalid transaction is rolled back (original cause: InvalidRequestError: Can't reconnect until invalid transaction is rolled back) 'UPDATE tool_dependency SET update_time=%s, status=%s, error_message=%s WHERE tool_dependency.id = %s' [{'status': 'Error', 'error_message': ' File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 110, in install_and_build_package_via_fabric\n tool_dependency = self.install_and_build_package( app, tool_shed_repository, tool_dependency, actions_dict )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 94, in install_and_build_package\n initial_download=False )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step\n initial_download=initial_download )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 510, in execute_step\n return_output=False )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 148, in handle_command\n context.flush()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do\n return getattr(self.registry(), name)(*args, **kwargs)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush\n self._flush(objects)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1807, in _flush\n transaction.rollback(_capture_exception=True)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 386, in rollback\n transaction._rollback_impl()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 414, in _rollback_impl\n t[1].rollback()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2034, in rollback\n self._do_rollback()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2071, in _do_rollback\n self.connection._rollback_impl()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1265, in _rollback_impl\n self._handle_dbapi_exception(e, None, None, None, None)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1262, in _rollback_impl\n self.engine.dialect.do_rollback(self.connection)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 1910, in do_rollback\n connection.rollback()\n\n(OperationalError) (2006, 'MySQL server has gone away') None None', u'tool_dependency_id': 326L}] URL: http://biominavm-galaxy.biomina.be/galaxy/admin_toolshed/manage_repositories File '/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 377 in decorator return func( self, trans, *args, **kwargs ) File '/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 724 in manage_repositories **decoded_kwd ) File '/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 377 in decorator return func( self, trans, *args, **kwargs ) File '/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 645 in install_tool_shed_repositories reinstalling=reinstalling ) File '/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/repository_util.py', line 629 in install_tool_shed_repository from_tool_migration_manager=False ) File '/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', line 566 in install_specified_tool_dependencies remove_installation_path=False ) File '/galaxy/galaxy-dist/lib/tool_shed/util/tool_dependency_util.py', line 400 in handle_tool_dependency_installation_error tool_shed_repository = tool_dependency.tool_shed_repository File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py', line 168 in __get__ File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py', line 453 in get File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py', line 490 in _load_for_state File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py', line 531 in _get_ident_for_use_get File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 1646 in _get_state_attr_by_column File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py', line 451 in get File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/state.py', line 285 in __call__ File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 1714 in _load_scalar_attributes File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2512 in _load_on_ident File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2184 in one File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2227 in __iter__ File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2240 in _execute_and_instances File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2231 in _connection_from_session File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', line 777 in connection close_with_result=close_with_result) File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', line 781 in _connection_for_bind return self.transaction._connection_for_bind(engine) File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', line 289 in _connection_for_bind self._assert_is_active() File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', line 213 in _assert_is_active % self._rollback_exception InvalidRequestError: This Session's transaction has been rolled back due to a previous exception during flush. To begin a new transaction with this Session, first issue Session.rollback(). Original exception was: Can't reconnect until invalid transaction is rolled back (original cause: InvalidRequestError: Can't reconnect until invalid transaction is rolled back) 'UPDATE tool_dependency SET update_time=%s, status=%s, error_message=%s WHERE tool_dependency.id = %s' [{'status': 'Error', 'error_message': ' File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 110, in install_and_build_package_via_fabric\n tool_dependency = self.install_and_build_package( app, tool_shed_repository, tool_dependency, actions_dict )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 94, in install_and_build_package\n initial_download=False )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step\n initial_download=initial_download )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 510, in execute_step\n return_output=False )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 148, in handle_command\n context.flush()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do\n return getattr(self.registry(), name)(*args, **kwargs)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush\n self._flush(objects)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1807, in _flush\n transaction.rollback(_capture_exception=True)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 386, in rollback\n transaction._rollback_impl()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 414, in _rollback_impl\n t[1].rollback()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2034, in rollback\n self._do_rollback()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2071, in _do_rollback\n self.connection._rollback_impl()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1265, in _rollback_impl\n self._handle_dbapi_exception(e, None, None, None, None)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1262, in _rollback_impl\n self.engine.dialect.do_rollback(self.connection)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 1910, in do_rollback\n connection.rollback()\n\n(OperationalError) (2006, 'MySQL server has gone away') None None', u'tool_dependency_id': 326L}]
CGI Variables ------------- CONTENT_LENGTH: '-1' CONTENT_TYPE: 'application/x-www-form-urlencoded; charset=UTF-8' HTTP_ACCEPT: 'text/html, */*; q=0.01' HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch' HTTP_ACCEPT_LANGUAGE: 'nl-NL,nl;q=0.8,en-US;q=0.6,en;q=0.4' HTTP_CACHE_CONTROL: 'max-age=0' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: '__utma=94419599.1127508766.1403299856.1403299856.1405949987.2; __utmz=94419599.1403299856.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none); galaxysession=6730c1c7f605dc205ea1a59142b8e9026339899a15206ea6665be6a34bb4fa5a635956369e96da7d' HTTP_HOST: 'biominavm-galaxy.biomina.be' HTTP_ORIGIN: 'http://biominavm-galaxy.biomina.be' HTTP_REFERER: 'http://biominavm-galaxy.biomina.be/galaxy/admin_toolshed/prepare_for_install' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/34.0.1847.116 Chrome/34.0.1847.116 Safari/537.36' HTTP_VIA: '1.1 biominavm-galaxy.biomina.be' HTTP_X_REQUESTED_WITH: 'XMLHttpRequest' PATH_INFO: '/admin_toolshed/manage_repositories' REMOTE_ADDR: '143.169.236.220' REQUEST_METHOD: 'POST' SCRIPT_NAME: '/galaxy' SERVER_NAME: 'biominavm-galaxy.biomina.be' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1'
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On Fri, Aug 1, 2014 at 4:16 AM, Geert Vandeweyer geert.vandeweyer2@uantwerpen.be wrote:
Hi,
I'm running into issues with our galaxy installation regarding the new_file_path setting:
1/ clean up :
Can I safely delete all contents in the tmp folder using a cronjob, or manually when galaxy is (not) running. I have gathered almost 700Gb and >72K files on data there apparently. I suppose they are remnants of crashed jobs
Mostly yes. The only caveat versus what you said is I wouldn't assume you can just delete files because Galaxy isn't running (unless you are using the local job manager) - so I would just delete files by age (anything older than 2 weeks or a month or something like that).
2/ Should it be accessible by all nodes
Since I have that much data there, I suppose it does. However, it would make sense to use a seperate (local /tmp/ ?) folder for toolshed actions such as installations. As an example, I tried to install the package_perl from the test toolshed. On our production server, hosting the new_file_path on a NFS share with the 700GB / 72K files, this process ran for over 24 hours, then crashed the main process with the error below. On my development box (laptop, no network drives, single galaxy process), the package installed in under five minutes.
Traditionally it has needed to be shared across the compute nodes and Galaxy because "extra" collected/discovered files were populated there - but I think all the dev team tools now write those files to the working directory instead. So I cannot think of a reason this needs to be shared - I assume it can be something like /tmp but I could certainly be wrong (anyone else have a more informed opinion?).
I am not sure what to say about the PERL error... I hadn't even occurred to me that the install framework used this directory. Hope the rest of my response was somewhat helpful though.
Hope this helps, -John
Best,
Geert
==========
tool_shed.galaxy_install.install_manager ERROR 2014-08-01 05:10:20,656 Error installing tool dependency perl version 5.18.1. Traceback (most recent call last): File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 110, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( app, tool_shed_repository, tool_dependency, actions_dict ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 94, in install_and_build_package initial_download=False ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step initial_download=initial_download ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 510, in execute_step return_output=False ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 148, in handle_command context.flush() File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush self._flush(objects) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1807, in _flush transaction.rollback(_capture_exception=True) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 386, in rollback transaction._rollback_impl() File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 414, in _rollback_impl t[1].rollback() File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2034, in rollback self._do_rollback() File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2071, in _do_rollback self.connection._rollback_impl() File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1265, in _rollback_impl self._handle_dbapi_exception(e, None, None, None, None) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1262, in _rollback_impl self.engine.dialect.do_rollback(self.connection) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 1910, in do_rollback connection.rollback() OperationalError: (OperationalError) (2006, 'MySQL server has gone away') None None tool_shed.util.common_install_util ERROR 2014-08-01 05:10:20,743 Error installing tool dependency perl version 5.18.1: Can't reconnect until invalid transaction is rolled back (original cause: InvalidRequestError: Can't reconnect until invalid transaction is rolled back) 'UPDATE tool_dependency SET update_time=%s, status=%s, error_message=%s WHERE tool_dependency.id = %s' [{'status': 'Error', 'error_message': ' File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 110, in install_and_build_package_via_fabric\n tool_dependency = self.install_and_build_package( app, tool_shed_repository, tool_dependency, actions_dict )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 94, in install_and_build_package\n initial_download=False )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step\n initial_download=initial_download )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 510, in execute_step\n return_output=False )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 148, in handle_command\n context.flush()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do\n return getattr(self.registry(), name)(*args, **kwargs)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush\n self._flush(objects)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1807, in _flush\n transaction.rollback(_capture_exception=True)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 386, in rollback\n transaction._rollback_impl()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 414, in _rollback_impl\n t[1].rollback()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2034, in rollback\n self._do_rollback()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2071, in _do_rollback\n self.connection._rollback_impl()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1265, in _rollback_impl\n self._handle_dbapi_exception(e, None, None, None, None)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1262, in _rollback_impl\n self.engine.dialect.do_rollback(self.connection)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 1910, in do_rollback\n connection.rollback()\n\n(OperationalError) (2006, 'MySQL server has gone away') None None', u'tool_dependency_id': 326L}] Traceback (most recent call last): File "/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py", line 554, in install_specified_tool_dependencies from_tool_migration_manager=from_tool_migration_manager ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 313, in install_package action_elem=None ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 176, in install_via_fabric tool_dependency = self.install_and_build_package_via_fabric( app, tool_shed_repository, tool_dependency, actions_dict ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 119, in install_and_build_package_via_fabric remove_installation_path=False ) File "/galaxy/galaxy-dist/lib/tool_shed/util/tool_dependency_util.py", line 423, in handle_tool_dependency_installation_error sa_session.flush() File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush self._flush(objects) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1789, in _flush flush_context.execute() File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py", line 331, in execute rec.execute(self) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py", line 475, in execute uow File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", line 59, in save_obj mapper, table, update) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", line 485, in _emit_update_statements execute(statement, params) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1449, in execute params) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1584, in _execute_clauseelement compiled_sql, distilled_params File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1651, in _execute_context None, None) File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1645, in _execute_context conn = self._revalidate_connection() File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1044, in _revalidate_connection "Can't reconnect until invalid " StatementError: Can't reconnect until invalid transaction is rolled back (original cause: InvalidRequestError: Can't reconnect until invalid transaction is rolled back) 'UPDATE tool_dependency SET update_time=%s, status=%s, error_message=%s WHERE tool_dependency.id = %s' [{'status': 'Error', 'error_message': ' File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 110, in install_and_build_package_via_fabric\n tool_dependency = self.install_and_build_package( app, tool_shed_repository, tool_dependency, actions_dict )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 94, in install_and_build_package\n initial_download=False )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step\n initial_download=initial_download )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 510, in execute_step\n return_output=False )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 148, in handle_command\n context.flush()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do\n return getattr(self.registry(), name)(*args, **kwargs)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush\n self._flush(objects)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1807, in _flush\n transaction.rollback(_capture_exception=True)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 386, in rollback\n transaction._rollback_impl()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 414, in _rollback_impl\n t[1].rollback()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2034, in rollback\n self._do_rollback()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2071, in _do_rollback\n self.connection._rollback_impl()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1265, in _rollback_impl\n self._handle_dbapi_exception(e, None, None, None, None)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1262, in _rollback_impl\n self.engine.dialect.do_rollback(self.connection)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 1910, in do_rollback\n connection.rollback()\n\n(OperationalError) (2006, 'MySQL server has gone away') None None', u'tool_dependency_id': 326L}] 143.169.236.220 - - [31/Jul/2014:14:54:50 +0200] "POST /galaxy/admin_toolshed/manage_repositories HTTP/1.1" 500 - "http://biominavm-galaxy.biomina.be/galaxy/admin_toolshed/prepare_for_install" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/34.0.1847.116 Chrome/34.0.1847.116 Safari/537.36" Error - <class 'sqlalchemy.exc.InvalidRequestError'>: This Session's transaction has been rolled back due to a previous exception during flush. To begin a new transaction with this Session, first issue Session.rollback(). Original exception was: Can't reconnect until invalid transaction is rolled back (original cause: InvalidRequestError: Can't reconnect until invalid transaction is rolled back) 'UPDATE tool_dependency SET update_time=%s, status=%s, error_message=%s WHERE tool_dependency.id = %s' [{'status': 'Error', 'error_message': ' File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 110, in install_and_build_package_via_fabric\n tool_dependency = self.install_and_build_package( app, tool_shed_repository, tool_dependency, actions_dict )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 94, in install_and_build_package\n initial_download=False )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step\n initial_download=initial_download )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 510, in execute_step\n return_output=False )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 148, in handle_command\n context.flush()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do\n return getattr(self.registry(), name)(*args, **kwargs)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush\n self._flush(objects)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1807, in _flush\n transaction.rollback(_capture_exception=True)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 386, in rollback\n transaction._rollback_impl()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 414, in _rollback_impl\n t[1].rollback()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2034, in rollback\n self._do_rollback()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2071, in _do_rollback\n self.connection._rollback_impl()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1265, in _rollback_impl\n self._handle_dbapi_exception(e, None, None, None, None)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1262, in _rollback_impl\n self.engine.dialect.do_rollback(self.connection)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 1910, in do_rollback\n connection.rollback()\n\n(OperationalError) (2006, 'MySQL server has gone away') None None', u'tool_dependency_id': 326L}] URL: http://biominavm-galaxy.biomina.be/galaxy/admin_toolshed/manage_repositories File '/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 377 in decorator return func( self, trans, *args, **kwargs ) File '/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 724 in manage_repositories **decoded_kwd ) File '/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 377 in decorator return func( self, trans, *args, **kwargs ) File '/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 645 in install_tool_shed_repositories reinstalling=reinstalling ) File '/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/repository_util.py', line 629 in install_tool_shed_repository from_tool_migration_manager=False ) File '/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', line 566 in install_specified_tool_dependencies remove_installation_path=False ) File '/galaxy/galaxy-dist/lib/tool_shed/util/tool_dependency_util.py', line 400 in handle_tool_dependency_installation_error tool_shed_repository = tool_dependency.tool_shed_repository File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py', line 168 in __get__ File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py', line 453 in get File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py', line 490 in _load_for_state File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py', line 531 in _get_ident_for_use_get File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 1646 in _get_state_attr_by_column File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py', line 451 in get File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/state.py', line 285 in __call__ File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 1714 in _load_scalar_attributes File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2512 in _load_on_ident File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2184 in one File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2227 in __iter__ File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2240 in _execute_and_instances File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2231 in _connection_from_session File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', line 777 in connection close_with_result=close_with_result) File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', line 781 in _connection_for_bind return self.transaction._connection_for_bind(engine) File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', line 289 in _connection_for_bind self._assert_is_active() File '/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', line 213 in _assert_is_active % self._rollback_exception InvalidRequestError: This Session's transaction has been rolled back due to a previous exception during flush. To begin a new transaction with this Session, first issue Session.rollback(). Original exception was: Can't reconnect until invalid transaction is rolled back (original cause: InvalidRequestError: Can't reconnect until invalid transaction is rolled back) 'UPDATE tool_dependency SET update_time=%s, status=%s, error_message=%s WHERE tool_dependency.id = %s' [{'status': 'Error', 'error_message': ' File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 110, in install_and_build_package_via_fabric\n tool_dependency = self.install_and_build_package( app, tool_shed_repository, tool_dependency, actions_dict )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 94, in install_and_build_package\n initial_download=False )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step\n initial_download=initial_download )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 510, in execute_step\n return_output=False )\n File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 148, in handle_command\n context.flush()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do\n return getattr(self.registry(), name)(*args, **kwargs)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush\n self._flush(objects)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1807, in _flush\n transaction.rollback(_capture_exception=True)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 386, in rollback\n transaction._rollback_impl()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 414, in _rollback_impl\n t[1].rollback()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2034, in rollback\n self._do_rollback()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2071, in _do_rollback\n self.connection._rollback_impl()\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1265, in _rollback_impl\n self._handle_dbapi_exception(e, None, None, None, None)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1262, in _rollback_impl\n self.engine.dialect.do_rollback(self.connection)\n File "/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 1910, in do_rollback\n connection.rollback()\n\n(OperationalError) (2006, 'MySQL server has gone away') None None', u'tool_dependency_id': 326L}]
CGI Variables
CONTENT_LENGTH: '-1' CONTENT_TYPE: 'application/x-www-form-urlencoded; charset=UTF-8' HTTP_ACCEPT: 'text/html, */*; q=0.01' HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch' HTTP_ACCEPT_LANGUAGE: 'nl-NL,nl;q=0.8,en-US;q=0.6,en;q=0.4' HTTP_CACHE_CONTROL: 'max-age=0' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: '__utma=94419599.1127508766.1403299856.1403299856.1405949987.2; __utmz=94419599.1403299856.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none); galaxysession=6730c1c7f605dc205ea1a59142b8e9026339899a15206ea6665be6a34bb4fa5a635956369e96da7d' HTTP_HOST: 'biominavm-galaxy.biomina.be' HTTP_ORIGIN: 'http://biominavm-galaxy.biomina.be' HTTP_REFERER: 'http://biominavm-galaxy.biomina.be/galaxy/admin_toolshed/prepare_for_install' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/34.0.1847.116 Chrome/34.0.1847.116 Safari/537.36' HTTP_VIA: '1.1 biominavm-galaxy.biomina.be' HTTP_X_REQUESTED_WITH: 'XMLHttpRequest' PATH_INFO: '/admin_toolshed/manage_repositories' REMOTE_ADDR: '143.169.236.220' REQUEST_METHOD: 'POST' SCRIPT_NAME: '/galaxy' SERVER_NAME: 'biominavm-galaxy.biomina.be' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1'
WSGI Variables
application: <paste.recursive.RecursiveMiddleware object at 0xad8c1d0> is_api_request: False paste.cookies: (SimpleCookie: __utma='94419599.1127508766.1403299856.1403299856.1405949987.2' __utmz='94419599.1403299856.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none)' galaxysession='6730c1c7f605dc205ea1a59142b8e9026339899a15206ea6665be6a34bb4fa5a635956369e96da7d', '__utma=94419599.1127508766.1403299856.1403299856.1405949987.2; __utmz=94419599.1403299856.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none); galaxysession=6730c1c7f605dc205ea1a59142b8e9026339899a15206ea6665be6a34bb4fa5a635956369e96da7d') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xa8df9d0> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x2ca6450> paste.recursive.forward: <paste.recursive.Forwarder from /galaxy> paste.recursive.include: <paste.recursive.Includer from /galaxy> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /galaxy> paste.recursive.script_name: '/galaxy' paste.throw_errors: True request_id: 'dc296d0a18b111e484a100163602f2ed' webob._parsed_post_vars: (MultiDict([('operation', 'install'), ('tool_shed_repository_ids', "['dc4272dc4bc65f47']"), ('encoded_kwd', '8466491acfb960dfb39d0377c52cdd7698cac2ef: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...t([('op...e')])>) webob._parsed_query_vars: (MultiDict([]), '') wsgi process: 'Multithreaded'
--
Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer
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Geert Vandeweyer -
John Chilton