Hi all, after successful configuration of multiple server instances (web and runner) I've placed everything behind apache proxy (actually I'm trying to). I can see the welcome page and navigate through my history (still I have to delegate the authentication to apache), nevertheless I'm not able to perform any job... getting data from UCSC is waiting for run after a couple of hours, uploading files is stuck... Hence I've tried to disable the proxy thing and still have the same issues. I've then checked at the log files for the five runners and two of them report this:
[runner0] serving on http://127.0.0.1:8100 galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 13:49:09,032 RoundRobin queue: user/session did not exist, created new jobqueue for session = 6galaxy.jobs DEBUG 2010-05-21 13:49:09,032 job 13 put in policy queue galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 13:49:09,032 RoundRobin queue: retrieving job from job queue for session = 6 galaxy.jobs DEBUG 2010-05-21 13:49:09,032 dispatching job 13 to local runner galaxy.jobs DEBUG 2010-05-21 13:49:09,135 job 13 dispatched galaxy.jobs.runners.local DEBUG 2010-05-21 13:49:09,538 executing: python /data/galaxy_dist/tools/data_source/data_source.py /data/galaxy_dist/database/files /000/dataset_60.dat 0 galaxy.jobs.runners.local ERROR 2010-05-21 13:49:09,761 Uncaught exception running job Traceback (most recent call last): File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 46, in run_next self.run_job( job_wrapper ) File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 101, in run_job job_wrapper.fail( "failure running job", exception=True ) File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 413, in fail self.sa_session.refresh( job ) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/session.py", line 929, in refresh only_load_props=attribute_names) is None: File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1500, in _get return q.all()[0] File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ return self._execute_and_instances(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 901, in __execute_context return context.get_result_proxy() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy return base.BufferedRowResultProxy(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1415, in __init__ self._init_metadata() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata self.__buffer_rows() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows self.__rowbuffer = self.cursor.fetchmany(size) File "/usr/lib/python2.5/decimal.py", line 541, in __new__ m = _parser(value) OperationalError: could not receive data from server: Error 0
[runner1] serving on http://127.0.0.1:8101 galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 13:49:09,198 RoundRobin queue: user/session did not exist, created new jobqueue for session = 6 galaxy.jobs DEBUG 2010-05-21 13:49:09,199 job 13 put in policy queue galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 13:49:09,199 RoundRobin queue: retrieving job from job queue for session = 6 galaxy.jobs DEBUG 2010-05-21 13:49:09,199 dispatching job 13 to local runner galaxy.jobs DEBUG 2010-05-21 13:49:09,315 job 13 dispatched galaxy.jobs.runners.local ERROR 2010-05-21 13:49:09,741 Uncaught exception running job Traceback (most recent call last): File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 46, in run_next self.run_job( job_wrapper ) File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 58, in run_job job_wrapper.fail( "failure preparing job", exception=True ) File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 413, in fail self.sa_session.refresh( job ) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/session.py", line 929, in refresh only_load_props=attribute_names) is None: File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1500, in _get return q.all()[0] File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ return self._execute_and_instances(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 901, in __execute_context return context.get_result_proxy() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy return base.BufferedRowResultProxy(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1415, in __init__ self._init_metadata() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata self.__buffer_rows() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows self.__rowbuffer = self.cursor.fetchmany(size) File "/usr/lib/python2.5/decimal.py", line 541, in __new__ m = _parser(value) OperationalError: could not receive data from server: Error 0
BTW, this is the proxy conf:
<IfModule mod_proxy.c>
ProxyRequests Off
ProxyVia Off <Proxy balancer://galaxy> BalancerMember http://localhost:8080 BalancerMember http://localhost:8081 </Proxy> </IfModule>
and the rewrite rules:
RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /data/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/(.*) /data/galaxy_dist/static/$1 [L] RewriteRule ^/galaxy/images/(.*) /data/galaxy_dist/static/images/$1 [L] RewriteRule ^/galaxy/favicon.ico /data/galaxy_dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /data/galaxy_dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://127.0.0.1:8080$1 [P]
Any hint is appreciated...
Thanks
d
/* Davide Cittaro
Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy
tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
Davide Cittaro wrote:
Hi all, after successful configuration of multiple server instances (web and runner) I've placed everything behind apache proxy (actually I'm trying to). I can see the welcome page and navigate through my history (still I have to delegate the authentication to apache), nevertheless I'm not able to perform any job... getting data from UCSC is waiting for run after a couple of hours, uploading files is stuck... Hence I've tried to disable the proxy thing and still have the same issues. I've then checked at the log files for the five runners and two of them report this:
[runner0]
...
[runner1]
This is most likely the problem. At present we only support a single job runner. Try only starting runner0 and see if it works.
--nate
BTW, this is the proxy conf:
<IfModule mod_proxy.c>
ProxyRequests Off ProxyVia Off <Proxy balancer://galaxy> BalancerMember http://localhost:8080 BalancerMember http://localhost:8081 </Proxy></IfModule>
and the rewrite rules:
RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /data/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/(.*) /data/galaxy_dist/static/$1 [L] RewriteRule ^/galaxy/images/(.*) /data/galaxy_dist/static/images/$1 [L] RewriteRule ^/galaxy/favicon.ico /data/galaxy_dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /data/galaxy_dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://127.0.0.1:8080$1 [P]
Any hint is appreciated...
Thanks
d
/* Davide Cittaro
Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy
tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it mailto:davide.cittaro@ifom-ieo-campus.it */
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
On May 21, 2010, at 3:20 PM, Nate Coraor wrote:
Davide Cittaro wrote:
Hi all, after successful configuration of multiple server instances (web and runner) I've placed everything behind apache proxy (actually I'm trying to). I can see the welcome page and navigate through my history (still I have to delegate the authentication to apache), nevertheless I'm not able to perform any job... getting data from UCSC is waiting for run after a couple of hours, uploading files is stuck... Hence I've tried to disable the proxy thing and still have the same issues. I've then checked at the log files for the five runners and two of them report this: [runner0]
...
[runner1]
This is most likely the problem. At present we only support a single job runner. Try only starting runner0 and see if it works.
Mmm...
galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 15:53:48,681 RoundRobin queue: inserted new job for user/session = 6 galaxy.jobs DEBUG 2010-05-21 15:53:48,681 job 24 put in policy queue galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 15:53:48,682 RoundRobin queue: retrieving job from job queue for session = 6 galaxy.jobs DEBUG 2010-05-21 15:53:48,682 dispatching job 24 to local runner galaxy.jobs DEBUG 2010-05-21 15:53:48,773 job 24 dispatched galaxy.jobs.runners.local DEBUG 2010-05-21 15:53:49,018 executing: python /data/galaxy_dist/tools/data_source/upload.py /tmp/tmphIrPuJ 71:/data/galaxy_dist/database/job_working_directory/24/dataset_71_files:/data/galaxy_dist/database/files/000/dataset_71.dat galaxy.jobs.runners.local DEBUG 2010-05-21 15:53:49,495 execution finished: python /data/galaxy_dist/tools/data_source/upload.py /tmp/tmphIrPuJ 71:/data/galaxy_dist/database/job_working_directory/24/dataset_71_files:/data/galaxy_dist/database/files/000/dataset_71.dat galaxy.jobs.runners.local ERROR 2010-05-21 15:53:49,689 Job wrapper finish method failed Traceback (most recent call last): File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 122, in run_job job_wrapper.finish( stdout, stderr ) File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 569, in finish self.sa_session.flush() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1356, in flush self._flush(objects) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1443, in _flush flush_context.finalize_flush_changes() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 288, in finalize_flush_changes self.session._register_newly_persistent(elem.state) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1015, in _register_newly_persistent instance_key = mapper._identity_key_from_state(state) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1085, in _identity_key_from_state return self.identity_key_from_primary_key(self._primary_key_from_state(state)) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1096, in _primary_key_from_state return [self._get_state_attr_by_column(state, column) for column in self.primary_key] File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1110, in _get_state_attr_by_column return self._get_col_to_prop(column).getattr(state, column) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/properties.py", line 99, in getattr return state.get_impl(self.key).get(state, state.dict) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get value = callable_() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/state.py", line 185, in __call__ attr.impl.key in unmodified File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1878, in _load_scalar_attributes result = session.query(mapper)._get(identity_key, refresh_state=state, only_load_props=attribute_names) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1500, in _get return q.all()[0] File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ return self._execute_and_instances(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 901, in __execute_context return context.get_result_proxy() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy return base.BufferedRowResultProxy(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1415, in __init__ self._init_metadata() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata self.__buffer_rows() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows self.__rowbuffer = self.cursor.fetchmany(size) File "/usr/local/lib/python2.6/decimal.py", line 540, in __new__ m = _parser(value.strip()) OperationalError: could not receive data from server: Error 0
galaxy.jobs.runners.local ERROR 2010-05-21 15:53:49,740 Uncaught exception running job Traceback (most recent call last): File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 46, in run_next self.run_job( job_wrapper ) File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 125, in run_job job_wrapper.fail("Unable to finish job", exception=True) File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 413, in fail self.sa_session.refresh( job ) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 929, in refresh only_load_props=attribute_names) is None: File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1500, in _get return q.all()[0] File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ return self._execute_and_instances(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 901, in __execute_context return context.get_result_proxy() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy return base.BufferedRowResultProxy(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1415, in __init__ self._init_metadata() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata self.__buffer_rows() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows self.__rowbuffer = self.cursor.fetchmany(size) File "/usr/local/lib/python2.6/decimal.py", line 540, in __new__ m = _parser(value.strip()) OperationalError: could not receive data from server: Error 0
d
/* Davide Cittaro
Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy
tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
Davide Cittaro wrote:
Mmm...
Do you happen to know how your Postgres was compiled? This can happen if --enable-thread-safety wasn't specified.
Also, if you're scrambling psycopg2 for a platform we don't provide, the bug could be in the way I've instructed the scramble script to compile the static libpq.
For Main on Solaris I build the egg by hand and dynamically link with the real Postgres install instead of statically linking our auto-compiled version:
PYTHONPATH=/path/to/galaxy/scripts/scramble/lib python setup.py build_ext --rpath=/usr/postgres/8.3/lib/64 egg_info --tag-build=_8.2.6_static bdist_egg
Also, is threadlocal enabled in the config?
database_engine_option_strategy = threadlocal
--nate
galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 15:53:48,681 RoundRobin queue: inserted new job for user/session = 6 galaxy.jobs DEBUG 2010-05-21 15:53:48,681 job 24 put in policy queue galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 15:53:48,682 RoundRobin queue: retrieving job from job queue for session = 6 galaxy.jobs DEBUG 2010-05-21 15:53:48,682 dispatching job 24 to local runner galaxy.jobs DEBUG 2010-05-21 15:53:48,773 job 24 dispatched galaxy.jobs.runners.local DEBUG 2010-05-21 15:53:49,018 executing: python /data/galaxy_dist/tools/data_source/upload.py /tmp/tmphIrPuJ
71:/data/galaxy_dist/database/job_working_directory/24/dataset_71_files:/data/galaxy_dist/database/files/000/dataset_71.dat
galaxy.jobs.runners.local DEBUG 2010-05-21 15:53:49,495 execution finished: python /data/galaxy_dist/tools/data_source/upload.py /tmp/tmphIrPuJ 71:/data/galaxy_dist/database/job_working_directory/24/dataset_71_files:/data/galaxy_dist/database/files/000/dataset_71.dat
galaxy.jobs.runners.local ERROR 2010-05-21 15:53:49,689 Job wrapper finish method failed Traceback (most recent call last): File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 122, in run_job job_wrapper.finish( stdout, stderr ) File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 569, in finish self.sa_session.flush() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1356, in flush self._flush(objects) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1443, in _flush flush_context.finalize_flush_changes() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 288, in finalize_flush_changes self.session._register_newly_persistent(elem.state) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1015, in _register_newly_persistent instance_key = mapper._identity_key_from_state(state) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1085, in _identity_key_from_state return self.identity_key_from_primary_key(self._primary_key_from_state(state)) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1096, in _primary_key_from_state return [self._get_state_attr_by_column(state, column) for column in self.primary_key] File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1110, in _get_state_attr_by_column return self._get_col_to_prop(column).getattr(state, column) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/properties.py", line 99, in getattr return state.get_impl(self.key).get(state, state.dict) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get value = callable_() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/state.py", line 185, in __call__ attr.impl.key in unmodified File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1878, in _load_scalar_attributes result = session.query(mapper)._get(identity_key, refresh_state=state, only_load_props=attribute_names) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1500, in _get return q.all()[0] File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ return self._execute_and_instances(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 901, in __execute_context return context.get_result_proxy() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy return base.BufferedRowResultProxy(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1415, in __init__ self._init_metadata() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata self.__buffer_rows() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows self.__rowbuffer = self.cursor.fetchmany(size) File "/usr/local/lib/python2.6/decimal.py", line 540, in __new__ m = _parser(value.strip()) OperationalError: could not receive data from server: Error 0
galaxy.jobs.runners.local ERROR 2010-05-21 15:53:49,740 Uncaught exception running job Traceback (most recent call last): File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 46, in run_next self.run_job( job_wrapper ) File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 125, in run_job job_wrapper.fail("Unable to finish job", exception=True) File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 413, in fail self.sa_session.refresh( job ) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 929, in refresh only_load_props=attribute_names) is None: File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1500, in _get return q.all()[0] File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ return self._execute_and_instances(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 901, in __execute_context return context.get_result_proxy() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy return base.BufferedRowResultProxy(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1415, in __init__ self._init_metadata() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata self.__buffer_rows() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows self.__rowbuffer = self.cursor.fetchmany(size) File "/usr/local/lib/python2.6/decimal.py", line 540, in __new__ m = _parser(value.strip()) OperationalError: could not receive data from server: Error 0
d
/* Davide Cittaro
Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy
tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it mailto:davide.cittaro@ifom-ieo-campus.it */
On May 21, 2010, at 4:38 PM, Nate Coraor wrote:
Davide Cittaro wrote:
Mmm...
Do you happen to know how your Postgres was compiled? This can happen if --enable-thread-safety wasn't specified.
Mmm.. I've installed the binary version provided for nexenta (i.e. apt-get install), I'll check for that
Also, if you're scrambling psycopg2 for a platform we don't provide, the bug could be in the way I've instructed the scramble script to compile the static libpq.
Using this psycopg2-2.0.13_8.4.2_static-py2.6-solaris-2.10-i86pc_64-ucs2.egg I see that you used postgres 8.4 while I have postgres 8.3.... Mmm... the strange fact is that, before trying the multiserver I was able to run some job...
For Main on Solaris I build the egg by hand and dynamically link with the real Postgres install instead of statically linking our auto-compiled version:
PYTHONPATH=/path/to/galaxy/scripts/scramble/lib python setup.py build_ext --rpath=/usr/postgres/8.3/lib/64 egg_info --tag-build=_8.2.6_static bdist_egg
I'll try that
Also, is threadlocal enabled in the config?
database_engine_option_strategy = threadlocal
It is
thanks
d
--nate
galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 15:53:48,681 RoundRobin queue: inserted new job for user/session = 6 galaxy.jobs DEBUG 2010-05-21 15:53:48,681 job 24 put in policy queue galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 15:53:48,682 RoundRobin queue: retrieving job from job queue for session = 6 galaxy.jobs DEBUG 2010-05-21 15:53:48,682 dispatching job 24 to local runner galaxy.jobs DEBUG 2010-05-21 15:53:48,773 job 24 dispatched galaxy.jobs.runners.local DEBUG 2010-05-21 15:53:49,018 executing: python /data/galaxy_dist/tools/data_source/upload.py /tmp/tmphIrPuJ 71:/data/galaxy_dist/database/job_working_directory/24/dataset_71_files:/data/galaxy_dist/database/files/000/dataset_71.dat galaxy.jobs.runners.local DEBUG 2010-05-21 15:53:49,495 execution finished: python /data/galaxy_dist/tools/data_source/upload.py /tmp/tmphIrPuJ 71:/data/galaxy_dist/database/job_working_directory/24/dataset_71_files:/data/galaxy_dist/database/files/000/dataset_71.dat galaxy.jobs.runners.local ERROR 2010-05-21 15:53:49,689 Job wrapper finish method failed Traceback (most recent call last): File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 122, in run_job job_wrapper.finish( stdout, stderr ) File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 569, in finish self.sa_session.flush() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1356, in flush self._flush(objects) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1443, in _flush flush_context.finalize_flush_changes() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 288, in finalize_flush_changes self.session._register_newly_persistent(elem.state) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1015, in _register_newly_persistent instance_key = mapper._identity_key_from_state(state) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1085, in _identity_key_from_state return self.identity_key_from_primary_key(self._primary_key_from_state(state)) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1096, in _primary_key_from_state return [self._get_state_attr_by_column(state, column) for column in self.primary_key] File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1110, in _get_state_attr_by_column return self._get_col_to_prop(column).getattr(state, column) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/properties.py", line 99, in getattr return state.get_impl(self.key).get(state, state.dict) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get value = callable_() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/state.py", line 185, in __call__ attr.impl.key in unmodified File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1878, in _load_scalar_attributes result = session.query(mapper)._get(identity_key, refresh_state=state, only_load_props=attribute_names) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1500, in _get return q.all()[0] File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ return self._execute_and_instances(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 901, in __execute_context return context.get_result_proxy() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy return base.BufferedRowResultProxy(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1415, in __init__ self._init_metadata() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata self.__buffer_rows() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows self.__rowbuffer = self.cursor.fetchmany(size) File "/usr/local/lib/python2.6/decimal.py", line 540, in __new__ m = _parser(value.strip()) OperationalError: could not receive data from server: Error 0 galaxy.jobs.runners.local ERROR 2010-05-21 15:53:49,740 Uncaught exception running job Traceback (most recent call last): File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 46, in run_next self.run_job( job_wrapper ) File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 125, in run_job job_wrapper.fail("Unable to finish job", exception=True) File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 413, in fail self.sa_session.refresh( job ) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 929, in refresh only_load_props=attribute_names) is None: File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1500, in _get return q.all()[0] File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ return self._execute_and_instances(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 901, in __execute_context return context.get_result_proxy() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy return base.BufferedRowResultProxy(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1415, in __init__ self._init_metadata() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata self.__buffer_rows() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows self.__rowbuffer = self.cursor.fetchmany(size) File "/usr/local/lib/python2.6/decimal.py", line 540, in __new__ m = _parser(value.strip()) OperationalError: could not receive data from server: Error 0 d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it mailto:davide.cittaro@ifom-ieo-campus.it */
/* Davide Cittaro
Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy
tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
Hi,
I have added a few tools in the galaxy.For one of these tools it sometime gives an error. but everytime I execute this tool it renders this exception on console.
Can anybody please help me fix it.
galaxy.jobs DEBUG 2010-05-21 14:30:03,166 dispatching job 203 to sge runner galaxy.jobs.runners.sge ERROR 2010-05-21 14:30:03,508 failure running job 203 Traceback (most recent call last): File "/export/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/sge.py", line 120, in queue_job job_wrapper.prepare() File "/export/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 390, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/export/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 1343, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/export/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1244, in __init__ self._compile(source, file, compilerSettings=compilerSettings) File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1538, in _compile keepRefToGeneratedCode=True) File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 745, in compile compiler.compile() File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Compiler.py", line 1670, in compile self._parser.parse() File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py", line 1488, in parse self.eatDirective() File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py", line 1610, in eatDirective directiveParser() File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py", line 1755, in eatEndDirective raise ParseError(self, msg='Invalid end directive') ParseError:
Invalid end directive Line 3, column 6
Line|Cheetah Code ----|------------------------------------------------------------- 2 | #else: #gkelvin $confile.nonmeta 3 | #end ^ 4 |
galaxy.jobs DEBUG 2010-05-21 14:30:03,509 job 203 dispatched
Regards, Amit Modi
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It looks to me like you might want to change the if/else to something like:
#if ## action #else # set $gkelvin $confile.nonmeta #end
I'm not certain exactly what you're trying to do, but I'm pretty sure that the two '#' on the same line without being a '##' to indicate a comment are part of the problem you're seeing below.
If that isn't what you're looking for, I recommend checking out the Cheetah users guide: http://www.cheetahtemplate.org/docs/users_guide_html/users_guide.html
On Fri, May 21, 2010 at 1:26 PM, Modi, Amit Amit.Modi@nationwidechildrens.org wrote:
Hi,
I have added a few tools in the galaxy.For one of these tools it sometime gives an error. but everytime I execute this tool it renders this exception on console.
Can anybody please help me fix it.
galaxy.jobs DEBUG 2010-05-21 14:30:03,166 dispatching job 203 to sge runner galaxy.jobs.runners.sge ERROR 2010-05-21 14:30:03,508 failure running job 203 Traceback (most recent call last): File "/export/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/sge.py", line 120, in queue_job job_wrapper.prepare() File "/export/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 390, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/export/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 1343, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/export/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1244, in __init__ self._compile(source, file, compilerSettings=compilerSettings) File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1538, in _compile keepRefToGeneratedCode=True) File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 745, in compile compiler.compile() File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Compiler.py", line 1670, in compile self._parser.parse() File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py", line 1488, in parse self.eatDirective() File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py", line 1610, in eatDirective directiveParser() File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py", line 1755, in eatEndDirective raise ParseError(self, msg='Invalid end directive') ParseError:
Invalid end directive Line 3, column 6
Line|Cheetah Code ----|------------------------------------------------------------- 2 | #else: #gkelvin $confile.nonmeta 3 | #end ^ 4 |
galaxy.jobs DEBUG 2010-05-21 14:30:03,509 job 203 dispatched
Regards, Amit Modi
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