Re: [galaxy-dev] FASTQ Groomer tool

2015-11-05 Thread Martin Čech 
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 
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
>

Re: [galaxy-dev] FASTQ Groomer tool

2015-11-05 Thread Martin Čech 
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/