Hello gents,
I just installed "FASTQ Groomer tool" for the teachers to try it out and I've been getting the following error than I do not understand:
galaxy.jobs DEBUG 2015-11-04 08:16:19,957 (756) Working directory for job is: /home/galaxy/galaxy-prod/database/job_working_directory/000/756 galaxy.jobs.handler WARNING 2015-11-04 08:16:19,958 (756) Tool 'toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4' removed from tool config, unable to run job galaxy.jobs.handler ERROR 2015-11-04 08:16:20,159 failure running job 756 Traceback (most recent call last): File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 273, in __monitor_step job_state = self.__check_job_state( job ) File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 342, in __check_job_state state, job_destination = self.__verify_job_ready( job, job_wrapper ) File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 362, in __verify_job_ready job_wrapper.fail( e ) File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/__init__.py", line 984, in fail self.sa_session.flush() File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/scoping.py", line 150, in do return getattr(self.registry(), name)(*args, **kwargs) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2004, in flush self._flush(objects) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2122, in _flush transaction.rollback(_capture_exception=True) File "build/bdist.linux-x86_64/egg/sqlalchemy/util/langhelpers.py", line 60, in __exit__ compat.reraise(exc_type, exc_value, exc_tb) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2086, in _flush flush_context.execute() File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 373, in execute rec.execute(self) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 532, in execute uow File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 170, in save_obj mapper, table, update) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 673, in _emit_update_statements execute(statement, multiparams) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 914, in execute return meth(self, multiparams, params) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement compiled_sql, distilled_params File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1146, in _execute_context context) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1332, in _handle_dbapi_exception exc_info File "build/bdist.linux-x86_64/egg/sqlalchemy/util/compat.py", line 199, in raise_from_cause reraise(type(exception), exception, tb=exc_tb) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1139, in _execute_context context) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 442, in do_execute cursor.execute(statement, parameters) File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py", line 173, in execute self.errorhandler(self, exc, value) File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py", line 36, in defaulterrorhandler raise errorclass, errorvalue ProgrammingError: (_mysql_exceptions.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 = 1498' at line 1") [SQL: u'UPDATE history_dataset_association SET update_time=%s, info=%s, blurb=%s WHERE history_dataset_association.id = %s'] [parameters: (datetime.datetime(2015, 11, 4, 13, 16, 20, 153739), ('This tool was disabled before the job completed. Please contact your Galaxy administrator.',), 'tool error', 1498L)]
According to the tool shed repo, fastq_groomer is installed properly. Mysql is at its latest for oracle linux 6: [0]# mysql --version mysql Ver 14.14 Distrib 5.1.73, for redhat-linux-gnu (x86_64) using readline 5.1
[0]# rpm -qa | grep -i mysql mysql-5.1.73-5.el6_6.x86_64
The only thing I have not done is update galaxy for the last 6 months because they're students using it and I do not want to change anything while it's in production. I'm a little bit lost: Would you please indicate what I should check next?
Cordialement / Regards,
Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568
Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218