Re: [galaxy-dev] FASTQ Groomer tool
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/sqlalchem
Re: [galaxy-dev] FASTQ Groomer tool
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/
[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
