- galaxy-dev - lists.galaxyproject.org

optional tool arguments
by Ryan G 29 Apr '15

29 Apr '15

Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or 2 fastq files as input. If 1 file is specified, then 1 output file is created. If 2 inputs are specified, then 2 output files will be created. How do I specify the optional output parameter? I'm using this as my tool description right now: <tool id="subsample_fastq" name="Random subsample"> <description>a fastq file</description> <command> ### Check for optional input file #if strlen($fq2) > 0: RandomSubFq -w $readsRequested -i "$fq1" -i "$fq2" -o $out1 -o $out2 #else: RandomSubFq -w $readsRequested -i "$fq1" -o $out1 #end if </command> <inputs> <param name="fq1" type="data" format="fastq" label="FASTQ file (1st of Pair)"/> <param name="fq2" type="data" format="fastq" label="FASTQ file (2nd of Pair)" optional="true"/> <param name="readsRequested" type="integer" min="1" value="100000" label="Total number of reads you want from the file"/> </inputs> <outputs> <data format="fastq" name="out1" /> <data format="fastq" name="out2" /> </outputs> <stdio> <exit_code range="-1" level="fatal" description="RandomSubFq failed" /> </stdio>

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Question about automated cleanup scripts
by Van Der Pol William 29 Apr '15

29 Apr '15

Hello, I had a quick question about how one of the cleanup scripts works. I was wondering if admin_cleanup_datasets.py will delete old datasets even if they have been shared or published. Thanks for the help -Liam

1 0

PR 149
by Roberto Alonso CIPF 29 Apr '15

29 Apr '15

Hello, I created a PR https://github.com/galaxyproject/galaxy/pull/149 dome days ago, but I don't have any feedback yet, is there any problem with it? Is it not interesting for the current Galaxy? didn't the authors realized about it? It would be nice to have some feedback, even if it is not a convenient PR. Thanks so much, Best regards -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain Tel: +34 963289680 Ext. 1021 Fax: +34 963289574 E-Mail: ralonso(a)cipf.es

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<code> tagset in tools
by Simon Gladman 29 Apr '15

29 Apr '15

Hi dev, Now that the <code> tagset is deprecated, how do we replace that functionality. For example the "get microbial data" tool runs the script listed in the <code> tagset to load the list of available microbe data when the tool is selected. This doesn't seem to work in the latest stable 15.03.1 or 15.03.2. How do we configure tools like this now? Or is there an updated version of the microbial_import tool? Cheers, Simon. -- Simon Gladman | Bioinformatician Victorian Life Sciences Computation Initiative - LSCC 187 Grattan Street, The University of Melbourne | Victoria 3010 Australia T +61 3 9035 5822 | M 0418 421 077 Mail: simon.gladman(a)unimelb.edu.au Web: http://www.vlsci.org.au

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UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped
by Peter Cock 29 Apr '15

29 Apr '15

Hi all, I think this is the second time I've have the following error on TravisCI (last time I reran a similar failure, and it worked). I've not yet re-run the test so that you can see the full error log: UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped https://travis-ci.org/peterjc/galaxy_blast/builds/60510547 My hunch is this is a race condition, perhaps with the SQLite database? Should I ask TravisCI to re-run the test and confirm this? Peter -- Except from the full log, ... <snip> ... galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,952 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,957 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,000 Enabling 'error' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,001 Enabling 'x-forwarded-host' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,002 Enabling 'Request ID' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,046 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.queue_worker INFO 2015-04-29 09:45:14,057 Initalizing Galaxy Queue Worker on sqlalchemy+sqlite:////tmp/tmpGyX8vL/tmpTRGC3O/database/universe.sqlite functional_tests.py DEBUG 2015-04-29 09:45:14,089 Attempting to serve app on randomly chosen port: 9572 Error - <class 'sqlalchemy.orm.exc.UnmappedClassError'>: Class 'kombu.transport.sqlalchemy.Message' is not mapped URL: http://localhost:9572/ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in handle_request trans = self.transaction_factory( environ ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 73 in <lambda> self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 104 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 205 in __init__ self._ensure_valid_session( session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 430 in _ensure_valid_session galaxy_session = self.__create_new_session( prev_galaxy_session, user_for_new_session ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 510 in __create_new_session referer=self.request.headers.get( 'Referer', None ) ) File '<string>', line 2 in __init__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 347 in _new_state_if_none File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py', line 747 in __get__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 177 in _state_constructor File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/event/attr.py', line 258 in __call__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2788 in _event_on_first_init File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2684 in configure_mappers File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 1706 in _post_configure_properties File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/interfaces.py', line 183 in init File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/relationships.py', line 1616 in do_init File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/relationships.py', line 1673 in _process_dependent_arguments File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py', line 747 in __get__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/relationships.py', line 1595 in mapper File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/base.py', line 426 in class_mapper UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT_ENCODING: 'identity' HTTP_HOST: 'localhost:9572' PATH_INFO: '/' REMOTE_ADDR: '127.0.0.1' REQUEST_METHOD: 'GET' SERVER_NAME: '127.0.0.1' SERVER_PORT: '9572' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0xa1a4e10> is_api_request: False paste.cookies: (<SimpleCookie: >, '') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xa1a4a90> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xa720d50> paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True request_id: '6f5c7eaaee5411e4bea1473d5f4e3057' wsgi process: 'Multithreaded' ------------------------------------------------------------ Exception in thread Thread-1: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 551, in __bootstrap_inner self.run() File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py", line 170, in run for _ in self.consume(limit=None): # pragma: no cover File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py", line 187, in consume with self.consumer_context(**kwargs) as (conn, channel, consumers): File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__ return self.gen.next() File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py", line 180, in consumer_context with self.Consumer() as (connection, channel, consumers): File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__ return self.gen.next() File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py", line 229, in Consumer with self._consume_from(*self.get_consumers(cls, channel)) as c: File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/queue_worker.py", line 53, in get_consumers callbacks=[self.process_task])] File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py", line 359, in __init__ self.revive(self.channel) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py", line 371, in revive self.declare() File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py", line 381, in declare queue.declare() File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/entity.py", line 505, in declare self.queue_declare(nowait, passive=False) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/entity.py", line 531, in queue_declare nowait=nowait) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/virtual/__init__.py", line 446, in queue_declare self._new_queue(queue, **kwargs) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/sqlalchemy/__init__.py", line 80, in _new_queue self._get_or_create(queue) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/sqlalchemy/__init__.py", line 68, in _get_or_create obj = self.session.query(self.queue_cls) \ File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1249, in query return self._query_cls(entities, self, **kwargs) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 110, in __init__ self._set_entities(entities) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 120, in _set_entities self._set_entity_selectables(self._entities) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 150, in _set_entity_selectables ent.setup_entity(*d[entity]) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 3184, in setup_entity self._with_polymorphic = ext_info.with_polymorphic_mappers File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py", line 747, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py", line 1889, in _with_polymorphic_mappers configure_mappers() File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py", line 2681, in configure_mappers raise e InvalidRequestError: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: Class 'kombu.transport.sqlalchemy.Message' is not mapped Error - <class 'sqlalchemy.exc.InvalidRequestError'>: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: Class 'kombu.transport.sqlalchemy.Message' is not mapped URL: http://localhost:9572/ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in handle_request trans = self.transaction_factory( environ ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 73 in <lambda> self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 104 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 205 in __init__ self._ensure_valid_session( session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 430 in _ensure_valid_session galaxy_session = self.__create_new_session( prev_galaxy_session, user_for_new_session ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 510 in __create_new_session referer=self.request.headers.get( 'Referer', None ) ) File '<string>', line 2 in __init__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 347 in _new_state_if_none File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py', line 747 in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 177 in _state_constructor File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/event/attr.py', line 258 in __call__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2788 in _event_on_first_init configure_mappers() File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2681 in configure_mappers raise e InvalidRequestError: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: Class 'kombu.transport.sqlalchemy.Message' is not mapped CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT_ENCODING: 'identity' HTTP_HOST: 'localhost:9572' PATH_INFO: '/' REMOTE_ADDR: '127.0.0.1' REQUEST_METHOD: 'GET' SERVER_NAME: '127.0.0.1' SERVER_PORT: '9572' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0xa1a4e10> is_api_request: False paste.cookies: (<SimpleCookie: >, '') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xa1a4a90> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xa720d50> paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True request_id: '6f72e654ee5411e490fc473d5f4e3057' wsgi process: 'Multithreaded' ------------------------------------------------------------ Error - <class 'sqlalchemy.exc.InvalidRequestError'>: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: Class 'kombu.transport.sqlalchemy.Message' is not mapped URL: http://localhost:9572/ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in handle_request trans = self.transaction_factory( environ ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 73 in <lambda> self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 104 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 205 in __init__ self._ensure_valid_session( session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 430 in _ensure_valid_session galaxy_session = self.__create_new_session( prev_galaxy_session, user_for_new_session ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 510 in __create_new_session referer=self.request.headers.get( 'Referer', None ) ) File '<string>', line 2 in __init__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 347 in _new_state_if_none File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py', line 747 in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 177 in _state_constructor File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/event/attr.py', line 258 in __call__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2788 in _event_on_first_init configure_mappers() File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2681 in configure_mappers raise e InvalidRequestError: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: Class 'kombu.transport.sqlalchemy.Message' is not mapped CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT_ENCODING: 'identity' HTTP_HOST: 'localhost:9572' PATH_INFO: '/' REMOTE_ADDR: '127.0.0.1' REQUEST_METHOD: 'GET' SERVER_NAME: '127.0.0.1' SERVER_PORT: '9572' SERVER_PROTOCOL: 'HTTP/1.1' (etc, repeats this a lot)

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follow up question regarding the 'toolform-upgrade'
by Hans-Rudolf Hotz 29 Apr '15

29 Apr '15

Hi all We just need some confirmation before we fix our tools: We have several local tools, where the input is a list of (gene)names with the following xml syntax: <param name="genenames" type="text" area="true" size="5x20" label="gene names" help="(one per line)"/> so far this, assuming you enterred: foo bar produced a string like: foo__cr____cn__bar__cr____cn__ Now, with "toolform-upgrade=True", we get: foo__cn__bar__cn__ (using firefox, with linux, Mac, and Windows) Can anybody confirm this (before we fix all affected tools) Thank you very much for your help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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Fwd: History panel error
by Jose Juan Almagro Armenteros 27 Apr '15

27 Apr '15

Hello Dannon, This is the log when a job is executed: galaxy.jobs DEBUG 2015-04-24 17:25:27,266 (9568) Working directory for job is: /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568 galaxy.jobs.handler DEBUG 2015-04-24 17:25:27,313 (9568) Dispatching to local runner galaxy.jobs DEBUG 2015-04-24 17:25:27,600 (9568) Persisting job destination (destination id: local) galaxy.jobs.handler INFO 2015-04-24 17:25:27,686 (9568) Job dispatched galaxy.jobs.runners DEBUG 2015-04-24 17:25:28,465 (9568) command is: python /steno-internal/projects/galaxy/galaxy-dist/tools/table_gen/generator.py "/steno-internal/projects/galaxy/galaxy-dist/database/files/021/dataset_21041.dat" "1"; return_code=$?; python /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/set_metadata_MH6prK.py /steno-internal/projects/galaxy/galaxy-dist/database/tmp/tmpw80FFi /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/galaxy.json /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_in_HistoryDatasetAssociation_14967_7w0ALE,/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_kwds_HistoryDatasetAssociation_14967_uH3ZBP,/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_out_HistoryDatasetAssociation_14967_5iEavP,/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_results_HistoryDatasetAssociation_14967_6FT2qV,/steno-internal/projects/galaxy/galaxy-dist/database/files/021/dataset_21041.dat,/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_override_HistoryDatasetAssociation_14967_iOPJoQ; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2015-04-24 17:25:28,475 (9568) executing job script: /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/galaxy_9568.sh galaxy.jobs DEBUG 2015-04-24 17:25:28,617 (9568) Persisting job destination (destination id: local) galaxy.jobs.runners.local DEBUG 2015-04-24 17:25:31,960 execution finished: /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/galaxy_9568.sh galaxy.datatypes.metadata DEBUG 2015-04-24 17:25:32,207 loading metadata from file for: HistoryDatasetAssociation 14967 galaxy.jobs INFO 2015-04-24 17:25:34,775 Collecting job metrics for <galaxy.model.Job object at 0x7f3154cacad0> galaxy.jobs DEBUG 2015-04-24 17:25:34,799 job 9568 ended galaxy.datatypes.metadata DEBUG 2015-04-24 17:25:34,800 Cleaning up external metadata files I am not sure at all but I think this is the internal error that I got with the history panel problem: 130.225.125.174 - - [24/Apr/2015:15:22:19 +0200] "GET /api/histories/32c70b5011288952/contents HTTP/1.1" 500 - " http://galaxy.bric.dk/history/view_multiple" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/37.0.2062.120 Safari/537.36" galaxy.web.framework.decorators ERROR 2015-04-24 15:22:20,033 Uncaught exception in exposed API method: Traceback (most recent call last): File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py", line 251, in decorator rval = func( self, trans, *args, **kwargs) File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/history_contents.py", line 105, in index hda_dict = self.hda_serializer.serialize_to_view( trans, content, view=view ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/managers/base.py", line 621, in serialize_to_view return self.serialize( trans, item, all_keys ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/managers/hdas.py", line 453, in serialize serialized = super( HDASerializer, self ).serialize( trans, hda, keys ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/managers/base.py", line 566, in serialize returned[ key ] = self.serializers[ key ]( trans, item, key ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/managers/hdas.py", line 403, in <lambda> 'resubmitted' : lambda t, i, k: i._state == t.app.model.Dataset.states.RESUBMITTED, AttributeError: 'Bunch' object has no attribute 'RESUBMITTED' Thanks a lot for your help! Regards, Jose 2015-04-24 17:16 GMT+02:00 Dannon Baker <dannon.baker(a)gmail.com>: > Hi Jose, > > Can you review (and share, maybe) the relevant part of the logs from when > you attempt to execute a job? It'd be worth it, if you still have the > logs, to know what the "Internal Server Error" indicated in your first > message was, as well. > > -Dannon > > On Fri, Apr 24, 2015 at 11:00 AM Jose Juan Almagro Armenteros < > jjalmagro(a)gmail.com> wrote: > >> Hi again, >> >> Now it is working, I just went back to the previous version and updated >> it again. All is okay except that the job table in the postgresql database >> is empty and is not being updated with new jobs (the problem is only with >> this table). I run manage_db.sh upgrade but nothing happened. >> >> Do you know what could be causing this? >> >> Thank you again! >> >> Best regards, >> >> Jose >> >> 2015-04-24 14:22 GMT+02:00 Jose Juan Almagro Armenteros < >> jjalmagro(a)gmail.com>: >> >>> Hello all, >>> >>> I have updated my Galaxy distribution today to the latest version 15.03 >>> and the history panel is not being shown. The history seems to be there but >>> Galaxy can't display the datasets. Even if I create a new history and I >>> run a tool the dataset is not shown. It is just displayed an error which >>> says: "An error occurred while getting updates from the server..." and the >>> details shows this: >>> >>> { >>> "agent": "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/37.0.2062.120 Safari/537.36", >>> "url": "http://galaxy.bric.ku.dk/history/view_multipl/api/histories/782c6cc7ec4cfd9…", >>> "data": "", >>> "options": { >>> "data": {}, >>> "silent": true, >>> "parse": true, >>> "emulateHTTP": false, >>> "emulateJSON": false >>> }, >>> "xhr": { >>> "readyState": 4, >>> "responseText": "{\"err_msg\": \"Uncaught exception in exposed API method:\", \"err_code\": 0}", >>> "responseJSON": { >>> "err_msg": "Uncaught exception in exposed API method:", >>> "err_code": 0 >>> }, >>> "status": 500, >>> "statusText": "Internal Server Error", >>> "responseHeaders": { >>> "Date": "Fri, 24 Apr 2015 12:09:40 GMT\r", >>> "cache-control": "max-age=0,no-cache,no-store\r", >>> "Transfer-Encoding": "chunked\r", >>> "Server": "PasteWSGIServer/0.5 Python/2.7.3\r", >>> "Connection": "close\r", >>> "x-frame-options": "SAMEORIGIN\r", >>> "content-type": "application/json\r" >>> } >>> }, >>> "source": [], >>> "user": { >>> "username": "jose", >>> "quota_percent": 0, >>> "total_disk_usage": 101352147, >>> "nice_total_disk_usage": "96.7 MB", >>> "email": "jjalmagro(a)gmail.com", >>> "is_admin": true, >>> "tags_used": [], >>> "model_class": "User", >>> "id": "72ad249754f05d26" >>> } >>> } >>> >>> Do you have any idea what could go wrong? >>> >>> Thank you and best regards, >>> >>> Jose >>> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > >

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SSL/LDAP configuration for CloudMan/Galaxy
by David Kovalic 27 Apr '15

27 Apr '15

Hi, We are interested in running CloudMan/Galaxy with SSL and LDAP. After searching around on the internet it seems like this is achievable and probably not too difficult, but there is no current complete “cookbook recipe” for doing so, so I thought it best to ask questions before I go ahead and break stuff :) As I understand: · ngnix needs to have the LDAP module added, as the standard CM ngnix build doesn’t include this · ngnix needs to have a custom ngnix.conf file which specifies the use of SSL and LDAP · Galaxy need to have a custom configuration universe_wsgi.ini for LDAP use By searching online I can’t clearly figure out: · How to recompile (and persist across CM cluster termination/restart) a new version of ngnix · The best way to maintain and specify a custom ngnix.conf. Is it possible to do this by placing the custom ngnix.conf in the cluster S3 bucket and adding a configuration line specifying its URL (e.g. "nginx_conf_contents: https://s3.amazonaws.com/[cm bucket ID]/ngnix.conf") in persistent_data.yaml file in the CM S3 bucket? · Where do I make the modifications such that the changes to universe_wsgi.ini persist across CM cluster termination/restart? It would be great to get some experienced insight on how best to complete this configuration, and have it persist. Any guidance would be greatly appreciated. Thanks, David Kovalic

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planemo questions
by Christian Brenninkmeijer 27 Apr '15

27 Apr '15

Hi All, If there is a separate planemo mailing list please point me there. I have been planing with planemo and find it a great tools. This gives me two questions. 1. Why does planemo lint say: "CHECK: Help contains valid reStructuredText." But not throw an error when there is NO such information 2. Is there a way to do a test when there are multiple output files. For example a tool ways writes to two different files. Thanks in advance Christian

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splitting bams bai
by Roberto Alonso CIPF 27 Apr '15

27 Apr '15

Hello, I am writing some code in Galaxy for splitting bams. Up to know, I am following the ideas that Marco Albuquerque proposed in this thread http://dev.list.galaxyproject.org/Parallelism-using-metadata-td4666763.html . He proposed three ways of splitting: 1) by_rname -> splits the bam into files based on the chromosome 2) by_interval -> splits the bam into files based on a defined bp length, and does so across the entire genome present in the BAM file 3) by_read -> splits the bam into files based on the number of reads encountered (if multiple files, all other files match the interval as the first) As I think the easiest is the first one, I started with this option. First of all , I had to change line 82 of lib/galaxy/jobs/splitters/multi.py as that "if" didn't let the code to continue (I talked this in another thread). Next, I had to do some changes in lib/galaxy/datatypes/binary.py. I added a method "split" that creates the json for the script extract_dataset_parts.sh. Here, in the next code you can see that I call samtools -H in order to get the chromosome names, now I realized that I can get that information directly from metadatas in the input_datasets variable, so in the future I will change this. def split(cls, input_datasets, subdir_generator_function, split_params): # 1) by_rname -> splits the bam into files based on the chromosome # 2) by_interval -> splits the bam into files based on a defined bp length, and does so across the entire genome present in the BAM file # 3) by_read -> splits the bam into files based on the number of reads encountered (if multiple files, all other files match the interval as the first) if split_params is None: return if len(input_datasets) > 1: raise Exception("BAM file splitting does not support multiple files") input_file = input_datasets[0].file_name if 'split_mode' not in split_params: raise Exception('Tool does not define a split mode') elif split_params['split_mode'] == 'by_rname': log.debug("Attemping to split BAM file %s by chromosome", input_file) #First get bam header params = ["samtools", "view", "-H", input_file] output = subprocess.Popen( params, stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[0] output = output.split("\n") chrList = [] #Get chromosome list from the header. for line in output: fields = line.strip().split("\t") if fields[0].startswith("@SQ") and fields[1].startswith("SN:"): chrList.append(fields[1].split("SN:")[1]) # Write json for extract_dataset_parts for chrName in chrList: try: part_dir = subdir_generator_function() base_name = os.path.basename(input_file) part_path = os.path.join(part_dir, base_name) split_data = dict(class_name='%s.%s' % (cls.__module__, cls.__name__), output_name=part_path, input_name=input_file, args=dict(chromosome=chrName)) f = open(os.path.join(part_dir, 'split_info_%s.json' % base_name), 'w') json.dump(split_data, f) f.close() except Exception, e: log.error("Error: " + str(e)) raise else: raise Exception('Unsupported split mode %s' % split_params['split_mode']) split = classmethod(split) Well, this works correctly and writes the json as expected. Now I have to write the code that is called by scripts/extract_dataset_part.py (inside of extract_dataset_parts.sh) "cls.*process_split_file*(data)". So I created the next two function in the Bam class: def *process_split_file*(data): """ This is called in the context of an external process launched by a Task (possibly not on the Galaxy machine) to create the input files for the Task. The parameters: data - a dict containing the contents of the split file """ args = data['args'] input_name = data['input_name'] output_name = data['output_name'] chromosome = args['chromosome'] commands = Bam.get_split_commands_chromosome(input_name, output_name, chromosome) for cmd in commands: if 0 != os.system(cmd): raise Exception("Executing '%s' failed" % cmd) return True process_split_file = staticmethod(process_split_file) def get_split_commands_chromosome(input_name, output_name, chromosome): params = ["samtools view -h " + input_name + " " + output_name + " " + chromosome] return params get_split_commands_chromosome = staticmethod(get_split_commands_chromosome) Which is my problem? That I need the .bai related with that dataset "input_name", I think is in a metadata table, but I don't know how to get it, Could you please help me with this? In any case, if you find that I am doing something wrong, or you have a better idea of implementing this, please don't hesitate to contact me. Best regards -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain Tel: +34 963289680 Ext. 1021 Fax: +34 963289574 E-Mail: ralonso(a)cipf.es

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