Hi Edgar,
it seems you are hitting this fail:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/handler.py#L124
which
hints that the tool is not properly loaded in the toolbox. Did you restart
the server and handlers after you installed the tool?
I cannot help with the MySQL as we do not usually test or run Galaxy on it.
I understand that you did not update your Galaxy for 6 months?
Thank you for using Galaxy.
Martin
On Thu, Nov 5, 2015 at 2:20 PM Fernandez Edgar <edgar.fernan...@umontreal.ca>
wrote:
> Hello again,
>
>
>
> I installed today the tool : fastq_all_to_sanger
>
> I get the same SQL error with that one too.
>
> Any ideas guys?
>
>
>
> Thank you!!!
>
>
>
> Cordialement / Regards,
>
> Edgar Fernandez
>
>
>
> *De :* Fernandez Edgar
> *Envoyé :* November-04-15 8:58 AM
> *À :* 'galaxy-...@bx.psu.edu'
> *Objet :* [galaxy-dev] FASTQ Groomer tool
>
>
>
> 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
>
>
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