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:
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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
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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:
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paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter
from /galaxy>
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paste.throw_errors: True
request_id: 'dc296d0a18b111e484a100163602f2ed'
webob._parsed_post_vars: (MultiDict([('operation', 'install'),
('tool_shed_repository_ids', "['dc4272dc4bc65f47']"), ('encoded_kwd',
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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: [email protected]
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer
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