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'


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.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer

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