Hi Edgar, to add to Martin's explanation, it is my understanding that only the web process from which the tool installation is initiated knows about the new tool. The other web and handler processes will know about it only after a restart.
Cheers, Nicola ---- Martin Čech ha scritto ---- >Hi Edgar, > > >Galaxy loads tools on start so if you install a tool it will show it in the >panel (because that config is independent and already updated) however the >toolbox will not have it yet until the restart. > > >I updated the wiki >(https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial) to >make it more clear. > > >Thank you for using Galaxy. > > >M. > >On Thu, Nov 5, 2015 at 3:01 PM Fernandez Edgar <edgar.fernan...@umontreal.ca> >wrote: > >Hello Nicola and Martin, > > > >The service galaxy restart worked. > >Can you guys give me a small explanation please? > >Just for my understanding… > > > >Cordialement / Regards, > >Edgar Fernandez > > > >De : Nicola Soranzo [mailto:nicola.sora...@gmail.com] De la part de Nicola >Soranzo >Envoyé : November-05-15 2:33 PM >À : Fernandez Edgar; galaxy-...@bx.psu.edu >Objet : Re: [galaxy-dev] FASTQ Groomer tool > > > >Hi Edgar, >you can try to restart Galaxy (both web and handler processes) and re-run the >tool. > >Cheers, >Nicola > >On 05/11/15 19:18, Fernandez Edgar 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 > > > > > > >___________________________________________________________ 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: >https://lists.galaxyproject.org/ 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: > https://lists.galaxyproject.org/ > >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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
