On Fri, Aug 1, 2014 at 4:16 AM, Geert Vandeweyer
<geert.vandewey...@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.vandewe...@ua.ac.be
> http://ua.ac.be/cognitivegenetics
> http://www.linkedin.com/in/geertvandeweyer
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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