Hi Folks,
So I managed to ran through the ansible. What I did was to remove certain
steps. For example, I don't need slurm-drmaa and docker, then I skipped the
update cache. After these minor changes, it finished successfully(?) with
an error message it ignored. Then I tried to access the UI, but nothing
worked. I pasted it below for your reference. If anyone has seen this
before, please help. :-)
Sorry for the beginner question, so once the ansible playbook ran
through...seems the galaxy and the postgresql etc were started. How do I
start/stop them manually? Do I have to run the playbook every time I want
to run galaxy or only after I modify the playbook? Also, if I don't look at
the log, I don't even know that the UI is at 127.0.0.1:4001. Is there any
documentation for this?
Thanks,
Rui
error message:
galaxy.web.stack INFO 2018-10-12 19:41:53,874 [p:102477,w:1,m:0]
[MainThread] Galaxy server instance 'main.web.1' is running
Starting server in PID 101567.
serving on uwsgi://127.0.0.1:4001
galaxy.jobs.handler ERROR 2018-10-12 19:42:48,487 [p:102477,w:1,m:0]
[JobHandlerQueue.monitor_thread] Exception in monitor_step
Traceback (most recent call last):
File "lib/galaxy/jobs/handler.py", line 213, in __monitor
self.__monitor_step()
File "lib/galaxy/jobs/handler.py", line 272, in __monitor_step
.order_by(model.Job.id).all()
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py",
line 2737, in all
return list(self)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py",
line 2889, in __iter__
return self._execute_and_instances(context)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py",
line 2912, in _execute_and_instances
result = conn.execute(querycontext.statement, self._params)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 948, in execute
return meth(self, multiparams, params)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py",
line 269, in _execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 1060, in _execute_clauseelement
compiled_sql, distilled_params
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 1200, in _execute_context
context)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 1413, in _handle_dbapi_exception
exc_info
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py",
line 203, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 1193, in _execute_context
context)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py",
line 507, in do_execute
cursor.execute(statement, parameters)
OperationalError: (psycopg2.OperationalError) server closed the connection
unexpectedly
This probably means the server terminated abnormally
before or while processing the request.
[SQL: 'SELECT EXISTS (SELECT history_dataset_association.id,
history_dataset_association.history_id,
history_dataset_association.dataset_id,
history_dataset_association.create_time,
history_dataset_association.update_time, history_dataset_association.state,
history_dataset_association.copied_from_history_dataset_association_id,
history_dataset_association.copied_from_library_dataset_dataset_association_id,
history_dataset_association.name, history_dataset_association.info,
history_dataset_association.blurb, history_dataset_association.peek,
history_dataset_association.tool_version,
history_dataset_association.extension,
history_dataset_association.metadata,
history_dataset_association.parent_id,
history_dataset_association.designation,
history_dataset_association.deleted, history_dataset_association.visible,
history_dataset_association.extended_metadata_id,
history_dataset_association.version, history_dataset_association.hid,
history_dataset_association.purged,
history_dataset_association.hidden_beneath_collection_instance_id \nFROM
history_dataset_association, job_to_output_dataset \nWHERE job.id =
job_to_output_dataset.job_id AND history_dataset_association.id =
job_to_output_dataset.dataset_id AND history_dataset_association.deleted =
true) AS anon_1, EXISTS (SELECT history_dataset_collection_association.id
\nFROM history
