I have recently updated my Galaxy instance to the January '15 release and I am having trouble getting new tools to run once I install them from the tool shed. There are no issues with installation and previously installed tools work without issue. It appears that jobs are not started, the full error in my handler.log is below.
I'd appreciate if anyone can give me some help on where to start looking to solve this issue.
Thanks in advance!
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galaxy.jobs.handler WARNING 2015-03-16 16:24:46,252 (315) Tool 'toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0' removed from tool config, unable to run job
galaxy.jobs.handler ERROR 2015-03-16 16:24:46,335 failure running job 315
Traceback (most recent call last):
File "/storage/home/galaxy/test/test-version/galaxy-dist/lib/galaxy/jobs/handler.py", line 273, in __monitor_step
job_state = self.__check_job_state( job )
File "/storage/home/galaxy/test/test-version/galaxy-dist/lib/galaxy/jobs/handler.py", line 342, in __check_job_state
state, job_destination = self.__verify_job_ready( job, job_wrapper )
File "/storage/home/galaxy/test/test-version/galaxy-dist/lib/galaxy/jobs/handler.py", line 362, in __verify_job_ready
job_wrapper.fail( e )
File "/storage/home/galaxy/test/test-version/galaxy-dist/lib/galaxy/jobs/__init__.py", line 920, in fail
self.sa_session.flush()
File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do
return getattr(self.registry(), name)(*args, **kwargs)
File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush
self._flush(objects)
File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1789, in _flush
flush_context.execute()
File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py", line 331, in execute
rec.execute(self)
File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py", line 475, in execute
uow
File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", line 59, in save_obj
mapper, table, update)
File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", line 485, in _emit_update_statements
execute(statement, params)
File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1449, in execute
params)
File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1584, in _execute_clauseelement
compiled_sql, distilled_params
File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1698, in _execute_context
context)
File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1691, in _execute_context
context)
File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 331, in do_execute
cursor.execute(statement, parameters)
File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/MySQL_python-1.2.3c1_5.1.41_static-py2.7-linux-x86_64-ucs4.egg/MySQLdb/cursors.py", line 173, in execute
self.errorhandler(self, exc, value)
File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/MySQL_python-1.2.3c1_5.1.41_static-py2.7-linux-x86_64-ucs4.egg/MySQLdb/connections.py", line 36, in defaulterrorhandler
raise errorclass, errorvalue
ProgrammingError: (ProgrammingError) (1064, "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '), blurb='tool error' WHERE history_dataset_association.id = 474' at line 1") 'UPDATE history_dataset_association SET update_time=%s, info=%s, blurb=%s WHERE history_dataset_association.id = %s' (datetime.datetime(2015, 3, 16, 16, 19, 4, 823905), ('This tool qwas disabled before the job completed. Please contact your Galaxy administrator.',), 'tool error', 474L)
