- galaxy-dev - lists.galaxyproject.org

"Could not save visualization" error with "June 23, 2011" release
by Hans-Rudolf Hotz 18 Aug '11

18 Aug '11

Hi I am pretty sure, this must have been discussed before, but again, I cannot find a hint/reference in the e-mail archive: If I install a new galaxy server using the "June 23, 2011" release (changeset: 5743:720455407d1c), I cannot save a visualization after adding a new track: I get a little pop-up window saying "Could not save visualization", if I click on 'ok' it pretends to start saving, but the web browser freezes. and I get the following error: URL: http://silicon.fmi.ch:8097/tracks/save File '/galaxy/galaxy_test/galaxy_dist/eggs/WebError-0.8a-py2.5.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/galaxy/galaxy_test/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/galaxy/galaxy_test/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/galaxy/galaxy_test/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_test/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_test/galaxy_dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_test/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 65 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) File '/galaxy/galaxy_test/galaxy_dist/lib/galaxy/web/controllers/tracks.py', line 580 in save "track_type": track['track_type'], KeyError: 'track_type' Is this a 'bug' in the "June 23, 2011" release ? By looking through the commits on galaxy central i found the 'changeset: 5750:b13d16085dfc' from Jun 27: "Add generic method for getting track type and use it when saving visualizations." I am now using the two 'fixed' files: ~/static/scripts/trackster.js ~/templates/tracks/browser.mako and it now seems to work, ie I can save the changed visualization. Was this the right fix? Thank you very much for your help Regards, Hans

2 1

Cufflinks with reference annotation and without reference annotation
by Crystal Goh 18 Aug '11

18 Aug '11

Hi, I am Crystal. I have some problem with Cuffdiff output. Hope can get some advice. Thanks. After aligning RNA-seq reads with Tophat, I used the Tophat output for Cufflinks. For Cufflinks, I tried two approaches and compared the results: 1st approach: Put zebrafish Ensembl GTF as reference annotation 2nd approach: without reference annotation. >From the output of above 2 approaches, I continued with Cuffcompare (with reference annotation) and Cuffdiff, Attached word document is the workflow and parameters I set for these 2 approaches. When I compared the output of Cuffdiff between these 2 approaches, a total of 48584 tracking id with class code "=" was observed in trancript FPKM tracking file from Approach 1, whereas there is only 1248 tracking id with class code '=' from Approach 2 (I attached transcript FPKM tracking files from approach 1 and 2) In my opinion, I should observe 48584 tracking id with class code '=' and additional tracking id with other class codes in transcript FPKM tracking file from Approach 2. Can I get advice on this? Thank you. Best regards, Crystal

2 1

Database scheme migration.
by michael burrell (TSL) 18 Aug '11

18 Aug '11

Good afternoon I am having some trouble updating our local galaxy, in summary it seems to fail. I have included the errors below and would really appreciate any assistance that could be offered. galaxy@jic55119:~/software/galaxy-ceneral$ sh manage_db.sh upgrade 57 -> 58... Migration script to create table for exporting histories to archives. (ProgrammingError) there is no unique constraint matching given keys for referenced table "job" '\nCREATE TABLE job_export_history_archive (\n\tid SERIAL NOT NULL, \n\tjob_id INTEGER, \n\thistory_id INTEGER, \n\tdataset_id INTEGER, \n\tcompressed BOOLEAN, \n\thistory_attrs_filename TEXT, \n\tdatasets_attrs_filename TEXT, \n\tjobs_attrs_filename TEXT, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(job_id) REFERENCES job (id), \n\t FOREIGN KEY(history_id) REFERENCES history (id), \n\t FOREIGN KEY(dataset_id) REFERENCES dataset (id)\n)\n\n' {} done 58 -> 59... ….INTERMEDIATE STEPS REMOVED NO ERRORS REPORTED…… 78 -> 79... Migration script to add the job_to_input_library_dataset table. Creating job_to_input_library_dataset table failed: (ProgrammingError) there is no unique constraint matching given keys for referenced table "job" '\nCREATE TABLE job_to_input_library_dataset (\n\tid SERIAL NOT NULL, \n\tjob_id INTEGER, \n\tldda_id INTEGER, \n\tname VARCHAR(255), \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(job_id) REFERENCES job (id), \n\t FOREIGN KEY(ldda_id) REFERENCES library_dataset_dataset_association (id)\n)\n\n' {} Done Further information galaxy@jic55119:~/software/galaxy-ceneral$ hg tip changeset: 5793:f2638528e904 tag: tip user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Jul 14 22:54:43 2011 +0200 summary: Fix bug in trackster filtering of GFF datasets. galaxy@jic55119:~/software/galaxy-ceneral$ python -V Python 2.6.6 galaxy@jic55119:~/software/galaxy-ceneral$ psql --version psql (PostgreSQL) 8.4.8

2 1

Galaxy Test visualization problem
by Crystal Goh 18 Aug '11

18 Aug '11

Hi, I am Crystal. I tried to visualize Tophat output (BAM and BED files) together with UCSC Zebrafish refgene track chr21.bam (downloaded from http://genome.ucsc.edu/cgi-bin/hgTables) using Visualization in Galaxy Test but nothing appeared. The workflow I did was: 1) selecting Visualization > New Track Browser 2) In New Track Browser, I select Zebrafish Jul. 2010 (Zv9/danRer7) (danRer7) for Reference genome build (dbkey) 3) Click continue 4) Option > Add tracks 5) Select 3 datasets (BAM, BED from tophat output and refgene track file) > insert 6) Select chromosome 21 Nothing can be seen. Jeremy, can I get advice on this? Thanks. Best regards, Crystal

1 0

Python bug?
by David Hoover 18 Aug '11

18 Aug '11

We've run into an error with the SAM to BAM converter. An error occurred running this job: Samtools Version: 0.1.15 (r949:203) Error extracting alignments from (/gs1/users/galaxy/pro/database/files/000/dataset_285.dat), requested number of bytes is more than a Python string can hold We are running 32-bit Python. Would this be the problem, or do we need a newer version of samtools? David Hoover Helix Systems Staff http://helix.nih.gov

2 1

Re: [galaxy-dev] Error after migrating to latest changeset
by Nate Coraor 18 Aug '11

18 Aug '11

michael burrell (TSL) wrote: > Good Morning Nate, > > Thanks for the response, I was not able to find a work around for this so > we redeployed a fresh version of galaxy. Any ideas what could have caused > this issue ? It looks like a database migration had failed but still incremented the database version. If you still have the database we could double check, although it may not be possible to determine how it happened regardless. --nate > > Thanks > > Michael. > > On 16/08/2011 20:05, "Nate Coraor" <nate(a)bx.psu.edu> wrote: > > >michael burrell (TSL) wrote: > >> Good Morning, > >> > >> I am getting a big problem with our production server when I upgrade to > >>the latest change set (it was quite out of date). I have attached quite > >>a long paster output to try and show whats going on, > >> > >> Our galaxy instance no longer seems to run jobs at all, they are not > >>allocated a job runner and the following is given in the paster log > >> > >> I look forwards to your assistance. > > > >Hi Michael, > > > >Sorry for the delay in response. Did you ever find a solution to your > >problem, or are you still experiencing it? > > > >Thanks, > >--nate > > > >> > >> Thanks > >> > >> Michael. > >> ====== > >> > >> galaxy.datatypes.registry DEBUG 2011-07-12 11:46:50,433 Loaded indexer: > >>INDEXER_Interval_0 > >> galaxy.jobs.runners.local INFO 2011-07-12 11:46:50,436 starting workers > >> galaxy.jobs.runners.local DEBUG 2011-07-12 11:46:50,437 5 workers ready > >> galaxy.jobs DEBUG 2011-07-12 11:46:50,438 Loaded job runner: > >>galaxy.jobs.runners.local:LocalJobRunner > >> galaxy.jobs.runners.drmaa DEBUG 2011-07-12 11:46:50,483 10 workers ready > >> galaxy.jobs DEBUG 2011-07-12 11:46:50,483 Loaded job runner: > >>galaxy.jobs.runners.drmaa:DRMAAJobRunner > >> galaxy.jobs INFO 2011-07-12 11:46:50,484 job manager started > >> galaxy.jobs DEBUG 2011-07-12 11:46:50,861 no runner: 4400 is still in > >>new state, adding to the jobs queue > >> galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4401 is still in > >>new state, adding to the jobs queue > >> galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4403 is still in > >>new state, adding to the jobs queue > >> galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4404 is still in > >>new state, adding to the jobs queue > >> galaxy.jobs INFO 2011-07-12 11:46:50,869 job stopper started > >> galaxy.sample_tracking.external_service_types DEBUG 2011-07-12 > >>11:46:50,872 Loaded external_service_type: Simple unknown sequencer 1.0.0 > >> galaxy.sample_tracking.external_service_types DEBUG 2011-07-12 > >>11:46:50,875 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,895 Enabling > >>'admin' controller, class: AdminGalaxy > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,898 Enabling > >>'async' controller, class: ASync > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,915 Enabling > >>'dataset' controller, class: DatasetInterface > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,917 Enabling > >>'error' controller, class: Error > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,920 Enabling > >>'forms' controller, class: Forms > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,924 Enabling > >>'history' controller, class: HistoryController > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,942 Enabling > >>'library' controller, class: Library > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,946 Enabling > >>'library_admin' controller, class: LibraryAdmin > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,947 Enabling > >>'library_common' controller, class: LibraryCommon > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,949 Enabling > >>'mobile' controller, class: Mobile > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,952 Enabling 'page' > >>controller, class: PageController > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,958 Enabling > >>'requests' controller, class: Requests > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,996 Enabling > >>'requests_admin' controller, class: RequestsAdmin > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,997 Enabling > >>'requests_common' controller, class: RequestsCommon > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,000 Enabling 'root' > >>controller, class: RootController > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,002 Enabling 'tag' > >>controller, class: TagsController > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,004 Enabling > >>'tool_runner' controller, class: ToolRunner > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,013 Enabling > >>'tracks' controller, class: TracksController > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,016 Enabling > >>'ucsc_proxy' controller, class: UCSCProxy > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,019 Enabling 'user' > >>controller, class: User > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,022 Enabling > >>'visualization' controller, class: VisualizationController > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,107 Enabling > >>'workflow' controller, class: WorkflowController > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,110 Enabling > >>'external_service' controller, class: ExternalService > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,112 Enabling > >>'external_services' controller, class: ExternalServiceController > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,115 Enabling > >>'request_type' controller, class: RequestType > >> galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,146 Enabling > >>'httpexceptions' middleware > >> galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,148 Enabling 'recursive' > >>middleware > >> galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,169 Enabling 'error' > >>middleware > >> galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,173 Enabling 'trans > >>logger' middleware > >> galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,173 Enabling 'config' > >>middleware > >> galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,174 Enabling > >>'x-forwarded-host' middleware > >> > >> Starting server in PID 3738. > >> serving on http://127.0.0.1:8080 > >> sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:00,942 > >>Error closing cursor: current transaction is aborted, commands ignored > >>until end of transaction block > >> > >> galaxy.jobs ERROR 2011-07-12 11:47:00,942 failure running job 4400 > >> Traceback (most recent call last): > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", > >>line 187, in __monitor_step > >> job_state = self.__check_if_ready_to_run( job ) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", > >>line 232, in __check_if_ready_to_run > >> for dataset_assoc in job.input_datasets + > >>job.input_library_datasets: > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__ > >> return self.impl.get(instance_state(instance), > >>instance_dict(instance)) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get > >> value = callable_() > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__ > >> result = q.all() > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all > >> return list(self) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ > >> return self._execute_and_instances(context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-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 > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute > >> clause, params or {}) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute > >> return Connection.executors[c](self, object, multiparams, params) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 874, in > >>_execute_clauseelement > >> return self.__execute_context(context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context > >> self._cursor_execute(context.cursor, context.statement, > >>context.parameters[0], context=context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute > >> self._handle_dbapi_exception(e, statement, parameters, cursor, > >>context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 931, in > >>_handle_dbapi_exception > >> raise exc.DBAPIError.instance(statement, parameters, e, > >>connection_invalidated=is_disconnect) > >> ProgrammingError: (ProgrammingError) relation > >>"job_to_input_library_dataset" does not exist > >> 'SELECT job_to_input_library_dataset.id AS > >>job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS > >>job_to_input_library_dataset_job_id, > >>job_to_input_library_dataset.ldda_id AS > >>job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name > >>AS job_to_input_library_dataset_name, > >>library_dataset_dataset_association_1.id AS > >>library_dataset_dataset_association_1_id, > >>library_dataset_dataset_association_1.library_dataset_id AS > >>library_dataset_dataset_association_1_library_dataset_id, > >>library_dataset_dataset_association_1.dataset_id AS > >>library_dataset_dataset_association_1_dataset_id, > >>library_dataset_dataset_association_1.create_time AS > >>library_dataset_dataset_association_1_create_time, > >>library_dataset_dataset_association_1.update_time AS > >>library_dataset_dataset_association_1_update_time, > >>library_dataset_dataset_association_1.state AS > >>library_dataset_dataset_association_1_state, > >>library_dataset_dataset_association_1.copied_from_history_dataset_associa > >>tion_id! > >> AS library_dataset_dataset_association_1_copied_from_history_1, > >>library_dataset_dataset_association_1.copied_from_library_dataset_dataset > >>_association_id AS > >>library_dataset_dataset_association_1_copied_from_library_2, > >>library_dataset_dataset_association_1.name AS > >>library_dataset_dataset_association_1_name, > >>library_dataset_dataset_association_1.info AS > >>library_dataset_dataset_association_1_info, > >>library_dataset_dataset_association_1.blurb AS > >>library_dataset_dataset_association_1_blurb, > >>library_dataset_dataset_association_1.peek AS > >>library_dataset_dataset_association_1_peek, > >>library_dataset_dataset_association_1.extension AS > >>library_dataset_dataset_association_1_extension, > >>library_dataset_dataset_association_1.metadata AS > >>library_dataset_dataset_association_1_metadata, > >>library_dataset_dataset_association_1.parent_id AS > >>library_dataset_dataset_association_1_parent_id, > >>library_dataset_dataset_association_1.designation AS > >>library_dataset_dataset_association_1_designation, librar! > >> y_dataset_dataset_association_1.deleted AS library_dataset_dat! > >> aset_ass > >> ociation_1_deleted, library_dataset_dataset_association_1.visible AS > >>library_dataset_dataset_association_1_visible, > >>library_dataset_dataset_association_1.user_id AS > >>library_dataset_dataset_association_1_user_id, > >>library_dataset_dataset_association_1.message AS > >>library_dataset_dataset_association_1_message \nFROM > >>job_to_input_library_dataset LEFT OUTER JOIN > >>library_dataset_dataset_association AS > >>library_dataset_dataset_association_1 ON > >>library_dataset_dataset_association_1.id = > >>job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = > >>job_to_input_library_dataset.job_id' {'param_1': 4400} > >> sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:00,978 > >>Error closing cursor: current transaction is aborted, commands ignored > >>until end of transaction block > >> > >> galaxy.jobs ERROR 2011-07-12 11:47:00,979 failure running job 4401 > >> Traceback (most recent call last): > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", > >>line 187, in __monitor_step > >> job_state = self.__check_if_ready_to_run( job ) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", > >>line 232, in __check_if_ready_to_run > >> for dataset_assoc in job.input_datasets + > >>job.input_library_datasets: > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__ > >> return self.impl.get(instance_state(instance), > >>instance_dict(instance)) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get > >> value = callable_() > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__ > >> result = q.all() > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all > >> return list(self) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ > >> return self._execute_and_instances(context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-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 > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute > >> clause, params or {}) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute > >> return Connection.executors[c](self, object, multiparams, params) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 874, in > >>_execute_clauseelement > >> return self.__execute_context(context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context > >> self._cursor_execute(context.cursor, context.statement, > >>context.parameters[0], context=context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute > >> self._handle_dbapi_exception(e, statement, parameters, cursor, > >>context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 931, in > >>_handle_dbapi_exception > >> raise exc.DBAPIError.instance(statement, parameters, e, > >>connection_invalidated=is_disconnect) > >> ProgrammingError: (ProgrammingError) relation > >>"job_to_input_library_dataset" does not exist > >> 'SELECT job_to_input_library_dataset.id AS > >>job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS > >>job_to_input_library_dataset_job_id, > >>job_to_input_library_dataset.ldda_id AS > >>job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name > >>AS job_to_input_library_dataset_name, > >>library_dataset_dataset_association_1.id AS > >>library_dataset_dataset_association_1_id, > >>library_dataset_dataset_association_1.library_dataset_id AS > >>library_dataset_dataset_association_1_library_dataset_id, > >>library_dataset_dataset_association_1.dataset_id AS > >>library_dataset_dataset_association_1_dataset_id, > >>library_dataset_dataset_association_1.create_time AS > >>library_dataset_dataset_association_1_create_time, > >>library_dataset_dataset_association_1.update_time AS > >>library_dataset_dataset_association_1_update_time, > >>library_dataset_dataset_association_1.state AS > >>library_dataset_dataset_association_1_state, > >>library_dataset_dataset_association_1.copied_from_history_dataset_associa > >>tion_id! > >> AS library_dataset_dataset_association_1_copied_from_history_1, > >>library_dataset_dataset_association_1.copied_from_library_dataset_dataset > >>_association_id AS > >>library_dataset_dataset_association_1_copied_from_library_2, > >>library_dataset_dataset_association_1.name AS > >>library_dataset_dataset_association_1_name, > >>library_dataset_dataset_association_1.info AS > >>library_dataset_dataset_association_1_info, > >>library_dataset_dataset_association_1.blurb AS > >>library_dataset_dataset_association_1_blurb, > >>library_dataset_dataset_association_1.peek AS > >>library_dataset_dataset_association_1_peek, > >>library_dataset_dataset_association_1.extension AS > >>library_dataset_dataset_association_1_extension, > >>library_dataset_dataset_association_1.metadata AS > >>library_dataset_dataset_association_1_metadata, > >>library_dataset_dataset_association_1.parent_id AS > >>library_dataset_dataset_association_1_parent_id, > >>library_dataset_dataset_association_1.designation AS > >>library_dataset_dataset_association_1_designation, librar! > >> y_dataset_dataset_association_1.deleted AS library_dataset_dat! > >> aset_ass > >> ociation_1_deleted, library_dataset_dataset_association_1.visible AS > >>library_dataset_dataset_association_1_visible, > >>library_dataset_dataset_association_1.user_id AS > >>library_dataset_dataset_association_1_user_id, > >>library_dataset_dataset_association_1.message AS > >>library_dataset_dataset_association_1_message \nFROM > >>job_to_input_library_dataset LEFT OUTER JOIN > >>library_dataset_dataset_association AS > >>library_dataset_dataset_association_1 ON > >>library_dataset_dataset_association_1.id = > >>job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = > >>job_to_input_library_dataset.job_id' {'param_1': 4401} > >> sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:00,999 > >>Error closing cursor: current transaction is aborted, commands ignored > >>until end of transaction block > >> > >> galaxy.jobs ERROR 2011-07-12 11:47:00,999 failure running job 4403 > >> Traceback (most recent call last): > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", > >>line 187, in __monitor_step > >> job_state = self.__check_if_ready_to_run( job ) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", > >>line 232, in __check_if_ready_to_run > >> for dataset_assoc in job.input_datasets + > >>job.input_library_datasets: > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__ > >> return self.impl.get(instance_state(instance), > >>instance_dict(instance)) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get > >> value = callable_() > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__ > >> result = q.all() > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all > >> return list(self) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ > >> return self._execute_and_instances(context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-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 > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute > >> clause, params or {}) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute > >> return Connection.executors[c](self, object, multiparams, params) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 874, in > >>_execute_clauseelement > >> return self.__execute_context(context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context > >> self._cursor_execute(context.cursor, context.statement, > >>context.parameters[0], context=context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute > >> self._handle_dbapi_exception(e, statement, parameters, cursor, > >>context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 931, in > >>_handle_dbapi_exception > >> raise exc.DBAPIError.instance(statement, parameters, e, > >>connection_invalidated=is_disconnect) > >> ProgrammingError: (ProgrammingError) relation > >>"job_to_input_library_dataset" does not exist > >> 'SELECT job_to_input_library_dataset.id AS > >>job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS > >>job_to_input_library_dataset_job_id, > >>job_to_input_library_dataset.ldda_id AS > >>job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name > >>AS job_to_input_library_dataset_name, > >>library_dataset_dataset_association_1.id AS > >>library_dataset_dataset_association_1_id, > >>library_dataset_dataset_association_1.library_dataset_id AS > >>library_dataset_dataset_association_1_library_dataset_id, > >>library_dataset_dataset_association_1.dataset_id AS > >>library_dataset_dataset_association_1_dataset_id, > >>library_dataset_dataset_association_1.create_time AS > >>library_dataset_dataset_association_1_create_time, > >>library_dataset_dataset_association_1.update_time AS > >>library_dataset_dataset_association_1_update_time, > >>library_dataset_dataset_association_1.state AS > >>library_dataset_dataset_association_1_state, > >>library_dataset_dataset_association_1.copied_from_history_dataset_associa > >>tion_id! > >> AS library_dataset_dataset_association_1_copied_from_history_1, > >>library_dataset_dataset_association_1.copied_from_library_dataset_dataset > >>_association_id AS > >>library_dataset_dataset_association_1_copied_from_library_2, > >>library_dataset_dataset_association_1.name AS > >>library_dataset_dataset_association_1_name, > >>library_dataset_dataset_association_1.info AS > >>library_dataset_dataset_association_1_info, > >>library_dataset_dataset_association_1.blurb AS > >>library_dataset_dataset_association_1_blurb, > >>library_dataset_dataset_association_1.peek AS > >>library_dataset_dataset_association_1_peek, > >>library_dataset_dataset_association_1.extension AS > >>library_dataset_dataset_association_1_extension, > >>library_dataset_dataset_association_1.metadata AS > >>library_dataset_dataset_association_1_metadata, > >>library_dataset_dataset_association_1.parent_id AS > >>library_dataset_dataset_association_1_parent_id, > >>library_dataset_dataset_association_1.designation AS > >>library_dataset_dataset_association_1_designation, librar! > >> y_dataset_dataset_association_1.deleted AS library_dataset_dat! > >> aset_ass > >> ociation_1_deleted, library_dataset_dataset_association_1.visible AS > >>library_dataset_dataset_association_1_visible, > >>library_dataset_dataset_association_1.user_id AS > >>library_dataset_dataset_association_1_user_id, > >>library_dataset_dataset_association_1.message AS > >>library_dataset_dataset_association_1_message \nFROM > >>job_to_input_library_dataset LEFT OUTER JOIN > >>library_dataset_dataset_association AS > >>library_dataset_dataset_association_1 ON > >>library_dataset_dataset_association_1.id = > >>job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = > >>job_to_input_library_dataset.job_id' {'param_1': 4403} > >> sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:01,027 > >>Error closing cursor: current transaction is aborted, commands ignored > >>until end of transaction block > >> > >> galaxy.jobs ERROR 2011-07-12 11:47:01,028 failure running job 4404 > >> Traceback (most recent call last): > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", > >>line 187, in __monitor_step > >> job_state = self.__check_if_ready_to_run( job ) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", > >>line 232, in __check_if_ready_to_run > >> for dataset_assoc in job.input_datasets + > >>job.input_library_datasets: > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__ > >> return self.impl.get(instance_state(instance), > >>instance_dict(instance)) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get > >> value = callable_() > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__ > >> result = q.all() > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all > >> return list(self) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ > >> return self._execute_and_instances(context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-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 > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute > >> clause, params or {}) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute > >> return Connection.executors[c](self, object, multiparams, params) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 874, in > >>_execute_clauseelement > >> return self.__execute_context(context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context > >> self._cursor_execute(context.cursor, context.statement, > >>context.parameters[0], context=context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute > >> self._handle_dbapi_exception(e, statement, parameters, cursor, > >>context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 931, in > >>_handle_dbapi_exception > >> raise exc.DBAPIError.instance(statement, parameters, e, > >>connection_invalidated=is_disconnect) > >> ProgrammingError: (ProgrammingError) relation > >>"job_to_input_library_dataset" does not exist > >> 'SELECT job_to_input_library_dataset.id AS > >>job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS > >>job_to_input_library_dataset_job_id, > >>job_to_input_library_dataset.ldda_id AS > >>job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name > >>AS job_to_input_library_dataset_name, > >>library_dataset_dataset_association_1.id AS > >>library_dataset_dataset_association_1_id, > >>library_dataset_dataset_association_1.library_dataset_id AS > >>library_dataset_dataset_association_1_library_dataset_id, > >>library_dataset_dataset_association_1.dataset_id AS > >>library_dataset_dataset_association_1_dataset_id, > >>library_dataset_dataset_association_1.create_time AS > >>library_dataset_dataset_association_1_create_time, > >>library_dataset_dataset_association_1.update_time AS > >>library_dataset_dataset_association_1_update_time, > >>library_dataset_dataset_association_1.state AS > >>library_dataset_dataset_association_1_state, > >>library_dataset_dataset_association_1.copied_from_history_dataset_associa > >>tion_id! > >> AS library_dataset_dataset_association_1_copied_from_history_1, > >>library_dataset_dataset_association_1.copied_from_library_dataset_dataset > >>_association_id AS > >>library_dataset_dataset_association_1_copied_from_library_2, > >>library_dataset_dataset_association_1.name AS > >>library_dataset_dataset_association_1_name, > >>library_dataset_dataset_association_1.info AS > >>library_dataset_dataset_association_1_info, > >>library_dataset_dataset_association_1.blurb AS > >>library_dataset_dataset_association_1_blurb, > >>library_dataset_dataset_association_1.peek AS > >>library_dataset_dataset_association_1_peek, > >>library_dataset_dataset_association_1.extension AS > >>library_dataset_dataset_association_1_extension, > >>library_dataset_dataset_association_1.metadata AS > >>library_dataset_dataset_association_1_metadata, > >>library_dataset_dataset_association_1.parent_id AS > >>library_dataset_dataset_association_1_parent_id, > >>library_dataset_dataset_association_1.designation AS > >>library_dataset_dataset_association_1_designation, librar! > >> y_dataset_dataset_association_1.deleted AS library_dataset_dat! > >> aset_ass > >> ociation_1_deleted, library_dataset_dataset_association_1.visible AS > >>library_dataset_dataset_association_1_visible, > >>library_dataset_dataset_association_1.user_id AS > >>library_dataset_dataset_association_1_user_id, > >>library_dataset_dataset_association_1.message AS > >>library_dataset_dataset_association_1_message \nFROM > >>job_to_input_library_dataset LEFT OUTER JOIN > >>library_dataset_dataset_association AS > >>library_dataset_dataset_association_1 ON > >>library_dataset_dataset_association_1.id = > >>job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = > >>job_to_input_library_dataset.job_id' {'param_1': 4404} > >> 149.155.218.28 - - [12/Jul/2011:11:47:31 +0100] "POST > >>/root/history_item_updates HTTP/1.1" 200 - > >>"http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac > >>OS X 10_6_8; en-us) AppleWebKit/533.21.1 (KHTML, like Gecko) > >>Version/5.0.5 Safari/533.21.1" > >> 149.155.221.116 - - [12/Jul/2011:11:47:33 +0100] "POST > >>/root/history_item_updates HTTP/1.1" 200 - > >>"http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac > >>OS X 10.6; en-GB; rv:1.9.2.19) Gecko/20110707 Firefox/3.6.19" > >> 149.155.221.194 - - [12/Jul/2011:11:47:33 +0100] "GET / HTTP/1.1" 200 - > >>"-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 > >>Firefox/5.0" > >> 149.155.221.194 - - [12/Jul/2011:11:47:33 +0100] "GET /history > >>HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/" "Mozilla/5.0 (Macintosh; > >>Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" > >> 149.155.221.194 - - [12/Jul/2011:11:47:33 +0100] "GET /root/tool_menu > >>HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/" "Mozilla/5.0 (Macintosh; > >>Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" > >> 149.155.218.28 - - [12/Jul/2011:11:47:35 +0100] "POST > >>/root/history_item_updates HTTP/1.1" 200 - > >>"http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac > >>OS X 10_6_8; en-us) AppleWebKit/533.21.1 (KHTML, like Gecko) > >>Version/5.0.5 Safari/533.21.1" > >> 149.155.221.116 - - [12/Jul/2011:11:47:37 +0100] "POST > >>/root/history_item_updates HTTP/1.1" 200 - > >>"http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac > >>OS X 10.6; en-GB; rv:1.9.2.19) Gecko/20110707 Firefox/3.6.19" > >> 149.155.221.194 - - [12/Jul/2011:11:47:36 +0100] "GET > >>/tool_runner/rerun?id=6014 HTTP/1.1" 200 - > >>"http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; Intel Mac OS > >>X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" > >> 149.155.221.194 - - [12/Jul/2011:11:47:38 +0100] "POST > >>/root/history_item_updates HTTP/1.1" 200 - > >>"http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; Intel Mac OS > >>X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" > >> 149.155.218.28 - - [12/Jul/2011:11:47:39 +0100] "POST > >>/root/history_item_updates HTTP/1.1" 200 - > >>"http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac > >>OS X 10_6_8; en-us) AppleWebKit/533.21.1 (KHTML, like Gecko) > >>Version/5.0.5 Safari/533.21.1" > >> 149.155.221.194 - - [12/Jul/2011:11:47:39 +0100] "POST > >>/tool_runner/index HTTP/1.1" 200 - > >>"http://galaxy.tsl.ac.uk/tool_runner/rerun?id=6014" "Mozilla/5.0 > >>(Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" > >> sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:40,371 > >>Error closing cursor: current transaction is aborted, commands ignored > >>until end of transaction block > >> > >> galaxy.jobs ERROR 2011-07-12 11:47:40,372 failure running job 4405 > >> Traceback (most recent call last): > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", > >>line 187, in __monitor_step > >> job_state = self.__check_if_ready_to_run( job ) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", > >>line 232, in __check_if_ready_to_run > >> for dataset_assoc in job.input_datasets + > >>job.input_library_datasets: > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__ > >> return self.impl.get(instance_state(instance), > >>instance_dict(instance)) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get > >> value = callable_() > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__ > >> result = q.all() > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all > >> return list(self) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ > >> return self._execute_and_instances(context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-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 > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute > >> clause, params or {}) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute > >> return Connection.executors[c](self, object, multiparams, params) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 874, in > >>_execute_clauseelement > >> return self.__execute_context(context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context > >> self._cursor_execute(context.cursor, context.statement, > >>context.parameters[0], context=context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute > >> self._handle_dbapi_exception(e, statement, parameters, cursor, > >>context) > >> File > >>"/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r649 > >>8-py2.6.egg/sqlalchemy/engine/base.py", line 931, in > >>_handle_dbapi_exception > >> raise exc.DBAPIError.instance(statement, parameters, e, > >>connection_invalidated=is_disconnect) > >> ProgrammingError: (ProgrammingError) relation > >>"job_to_input_library_dataset" does not exist > >> 'SELECT job_to_input_library_dataset.id AS > >>job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS > >>job_to_input_library_dataset_job_id, > >>job_to_input_library_dataset.ldda_id AS > >>job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name > >>AS job_to_input_library_dataset_name, > >>library_dataset_dataset_association_1.id AS > >>library_dataset_dataset_association_1_id, > >>library_dataset_dataset_association_1.library_dataset_id AS > >>library_dataset_dataset_association_1_library_dataset_id, > >>library_dataset_dataset_association_1.dataset_id AS > >>library_dataset_dataset_association_1_dataset_id, > >>library_dataset_dataset_association_1.create_time AS > >>library_dataset_dataset_association_1_create_time, > >>library_dataset_dataset_association_1.update_time AS > >>library_dataset_dataset_association_1_update_time, > >>library_dataset_dataset_association_1.state AS > >>library_dataset_dataset_association_1_state, > >>library_dataset_dataset_association_1.copied_from_history_dataset_associa > >>tion_id! > >> AS library_dataset_dataset_association_1_copied_from_history_1, > >>library_dataset_dataset_association_1.copied_from_library_dataset_dataset > >>_association_id AS > >>library_dataset_dataset_association_1_copied_from_library_2, > >>library_dataset_dataset_association_1.name AS > >>library_dataset_dataset_association_1_name, > >>library_dataset_dataset_association_1.info AS > >>library_dataset_dataset_association_1_info, > >>library_dataset_dataset_association_1.blurb AS > >>library_dataset_dataset_association_1_blurb, > >>library_dataset_dataset_association_1.peek AS > >>library_dataset_dataset_association_1_peek, > >>library_dataset_dataset_association_1.extension AS > >>library_dataset_dataset_association_1_extension, > >>library_dataset_dataset_association_1.metadata AS > >>library_dataset_dataset_association_1_metadata, > >>library_dataset_dataset_association_1.parent_id AS > >>library_dataset_dataset_association_1_parent_id, > >>library_dataset_dataset_association_1.designation AS > >>library_dataset_dataset_association_1_designation, librar! > >> y_dataset_dataset_association_1.deleted AS library_dataset_dat! > >> aset_ass > >> ociation_1_deleted, library_dataset_dataset_association_1.visible AS > >>library_dataset_dataset_association_1_visible, > >>library_dataset_dataset_association_1.user_id AS > >>library_dataset_dataset_association_1_user_id, > >>library_dataset_dataset_association_1.message AS > >>library_dataset_dataset_association_1_message \nFROM > >>job_to_input_library_dataset LEFT OUTER JOIN > >>library_dataset_dataset_association AS > >>library_dataset_dataset_association_1 ON > >>library_dataset_dataset_association_1.id = > >>job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = > >>job_to_input_library_dataset.job_id' {'param_1': 4405} > >> 149.155.221.194 - - [12/Jul/2011:11:47:40 +0100] "GET > >>/user/get_most_recently_used_tool_async HTTP/1.1" 200 - > >>"http://galaxy.tsl.ac.uk/root/tool_menu" "Mozilla/5.0 (Macintosh; Intel > >>Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" > >> 149.155.221.194 - - [12/Jul/2011:11:47:40 +0100] "GET /history > >>HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/tool_runner/index" "Mozilla/5.0 > >>(Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" > >> 149.155.221.116 - - [12/Jul/2011:11:47:41 +0100] "POST > >>/root/history_item_updates HTTP/1.1" 200 - > >>"http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac > >>OS X 10.6; en-GB; rv:1.9.2.19) Gecko/20110707 Firefox/3.6.19" > >> 149.155.221.194 - - [12/Jul/2011:11:47:42 +0100] "GET > >>/root/delete_async?id=6014 HTTP/1.1" 200 - > >>"http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; Intel Mac OS > >>X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" > >> 149.155.218.28 - - [12/Jul/2011:11:47:43 +0100] "POST > >>/root/history_item_updates HTTP/1.1" 200 - > >>"http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac > >>OS X 10_6_8; en-us) AppleWebKit/533.21.1 (KHTML, like Gecko) > >>Version/5.0.5 Safari/533.21.1" > >> > >> > >> ___________________________________________________________ > >> 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: > >> > >> http://lists.bx.psu.edu/ > >

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Re: [galaxy-dev] [galaxy-user] scramble pbs_python egg
by Nate Coraor 18 Aug '11

18 Aug '11

Luobin Yang wrote: > Hi, > > I am trying to scramble the pbs_python egg for my galaxy installation, when > I execute the following command: > > "LIBTORQUE_DIR=/usr/local/lib python scripts/scramble.py pbs_python" > > I got lots messages like the following: > > scramble(): Egg already exists, remove to force rebuild: > > /home/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-i686-ucs4.egg > ......... > > but there is message about pbs_python and there is no pbs_python.egg > generated in the eggs directory Hi Luobin, I've moved this discussion to the galaxy-dev list since it concerns a local installation. Sorry for the delay in response, if you've already resolved this issue please let us know. If not, please try the following: LIBTORQUE_DIR=/usr/local/lib python scripts/scramble.py -e pbs_python And paste the full output here if it fails. Thanks, --nate > > Anything wrong? > > Thanks, > Luobin > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/

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Tool parameters conditional on input datatype (format)
by Peter Cock 17 Aug '11

17 Aug '11

Hi all, Is it possible to have conditional/when tags which rather than working on select parameter's value work off an input file's type? e.g. In the "Extract Genomic DNA" tool, the parameter "Interpret features when possible" only applies when the input annotation is of GFF type, not BED format. It would be elegant to make this parameter conditional on the format. I appreciate this becomes fiddly due to the nested subclassing of the datatype names, e.g. Something of type GFF3 is also GFF and also text, which complicates things. I don't see anything like this on the wiki page, should I file an issue? http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax Thanks, Peter

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problems with "Access Libraries stored locally" tool
by Hans-Rudolf Hotz 17 Aug '11

17 Aug '11

Hi I apologize, if this problem has already been solved/discussed. I went through the e-mail repos, but couldn't find anything. With a little delay, I am in the process of upgrading our local Galaxy server. Currently, I am running a few tests with the "June 23, 2011 (720455407d1c)" release. I noticed the following problem during start-up of a fresh download: galaxy.tools DEBUG 2011-08-16 16:15:06,567 Loading section: SNP/WGA: Data; Filters galaxy.tools DEBUG 2011-08-16 16:15:06,630 Loaded tool: upload1 1.1.3 galaxy.tools ERROR 2011-08-16 16:15:06,639 error reading tool from path: data_source/access_libraries.xml Traceback (most recent call last): File "/galaxy/galaxy_test/galaxy_dist/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/galaxy/galaxy_test/galaxy_dist/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/galaxy/galaxy_test/galaxy_dist/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/galaxy/galaxy_test/galaxy_dist/lib/galaxy/tools/__init__.py", line 385, in parse self.interpreter = command.get("interpreter", None) AttributeError: 'NoneType' object has no attribute 'get' galaxy.tools DEBUG 2011-08-16 16:15:06,687 Loaded tool: rgClean1 1.0.0 and as a consequence: the tool "Access Libraries stored locally" is not available. Does anybody know, what went wrong? - The "__init__.py" is a little bit too big of a beast for me ;) We use this tool quite a lot for general access to data libraries (in addition to the drop down in the top menu bar) Thank you very much for any help Regards, Hans

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Modifying how runtime inputs are resolved when running a workflow
by Duddy, John 17 Aug '11

17 Aug '11

This is probably something only the Galaxy devs can answer, but I thought I'd give it a shot in the wider community. Some of you are doing some very complicated stuff. If you have a workflow with several input blocks, you might have multiple fastq files you need to provide. A good example of this is paired-end analysis - it doesn't really matter in which order you provide the fastq files for R1 and R2, but providing just one or the other twice requires user intervention. It would be really nice if Galaxy assigned a unique value from the history to runtime parameters (tool params and input modules) before reusing datasets. I'm trying to get the initial form for running a workflow as close as possible to "right" to reduce the number of steps a user has to go through. So, in this example, R1 would be assigned to one input and R2 to another (or the reverse), as the initial defaults. Is that what the "context" parameter of ToolParameter.get_initial_value() is for? I see that is used for repeat-group and conditionals, but it's used to store all the eligible values, not just the ones chosen from the history so far. For other tools, it accumulates the input values chosen for the tool. Would it be consistent with the design to modify templates/workflow/run.mako to accumulate a dictionary of datasets used, instead of clearing it for each module? Since InputDataModule uses DataToolParameter, I think I can make the change in DataToolParameter and get input blocks and tools in one fell swoop, and history items would not be reused across the entire workflow, providing the number of runtime parameters did not exceed the number of compatible history items. John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy(a)illumina.com<mailto:jduddy@illumina.com>

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