Re: [galaxy-dev] FASTQ Groomer tool
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-dev@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
Hi Edgar, it seems you are hitting this fail: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/handler.py#... 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.fernandez@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-dev@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/
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-dev@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/
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.soranzo@gmail.com] De la part de Nicola Soranzo Envoyé : November-05-15 2:33 PM À : Fernandez Edgar; galaxy-dev@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-dev@bx.psu.edu<mailto:galaxy-dev@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/
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.fernandez@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.soranzo@gmail.com] *De la part de* Nicola Soranzo *Envoyé :* November-05-15 2:33 PM *À :* Fernandez Edgar; galaxy-dev@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-dev@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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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.fernandez@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.soranzo@gmail.com] De la part de Nicola Soranzo Envoyé : November-05-15 2:33 PM À : Fernandez Edgar; galaxy-dev@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-dev@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/
participants (3)
-
Fernandez Edgar -
Martin Čech -
Nicola Soranzo