Hi, Posted this too quick: just realized that the jobs are actually created although I am getting this error.
bw C On 16 Jan 2013, at 13:55, Charles Girardot wrote: > Hi, > > I have a workflow that I can successfully launch on a single FASTQ (the only > input of the workflow). I am now trying to start the workflow on 8 different > FASTQ files (after demultiplexing) but systematically get this error (local > galaxy install): > > Thx for your help > > Charles > > URL: http://manni/galaxy/workflow/run > Module paste.exceptions.errormiddleware:143 in __call__ >>> app_iter = self.application(environ, start_response) > Module paste.debug.prints:98 in __call__ >>> environ, self.app) > Module paste.wsgilib:539 in intercept_output >>> app_iter = application(environ, replacement_start_response) > Module paste.recursive:80 in __call__ >>> return self.application(environ, start_response) > Module galaxy.web.framework.middleware.remoteuser:91 in __call__ >>> return self.app( environ, start_response ) > Module paste.httpexceptions:632 in __call__ >>> return self.application(environ, start_response) > Module galaxy.web.framework.base:160 in __call__ >>> body = method( trans, **kwargs ) > TypeError: run() takes at least 3 arguments (2 given) > > > ###### below is a copy-paste of all variables (if useful): > > CONTENT_LENGTH '0' > HTTP_ACCEPT > 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' > HTTP_ACCEPT_ENCODING 'gzip, deflate' > HTTP_ACCEPT_LANGUAGE 'en-us' > HTTP_AUTHORIZATION 'Basic Z2lyYXJkb3Q6Y3QwMmhlODg=' > HTTP_CONNECTION 'Keep-Alive' > HTTP_COOKIE > 'galaxysession=7df64c2bf0628c5b57afd358adee6e7b2cd6161345bb6b47388e497cbd26f407876c2bed128d9226;wikidb_ngs_Token=1f38fe6b5eb5863596cad189f608835c; > wikidb_ngs_UserName=Girardot; wikidb_ngs_UserID=15; > wikidb_ngs__session=d9n3qq68n0nl6p6j9t96k5q6m3' > HTTP_HOST 'manni' > HTTP_REFERER 'http://manni/galaxy/workflow/run?id=52d6640a458dfabe' > HTTP_REMOTE_USER 'girar...@embl.de' > HTTP_USER_AGENT 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) > AppleWebKit/534.57.2 (KHTML, like Gecko) Version/5.1.7 Safari/534.57.2' > PATH_INFO '/workflow/run' > REMOTE_ADDR '10.11.72.108' > REQUEST_METHOD 'GET' > SCRIPT_NAME '/galaxy' > SERVER_NAME 'manni' > SERVER_PORT '8080' > SERVER_PROTOCOL 'HTTP/1.1' > > Configuration > __file__ '/g/funcgen/galaxy/universe_wsgi.combined.ini' > admin_users 's...@embl.de,sa...@embl.de,girar...@embl.de,gal...@embl.de' > allow_library_path_paste 'True' > allow_user_dataset_purge 'True' > allow_user_impersonation 'True' > api_allow_run_as 'gal...@embl.de' > cleanup_job 'always' > cluster_files_directory '/g/galaxy/galaxy_data/pbs' > collect_outputs_from 'new_file_path,job_working_directory' > cookie_path '/galaxy' > database_connection 'postgres://galaxy:galaxy@manni/galaxy_db' > database_engine_option_max_overflow '20' > database_engine_option_pool_size '10' > database_engine_option_server_side_cursors 'True' > database_engine_option_strategy 'threadlocal' > debug 'True' > default_cluster_job_runner 'drmaa://-q gbcs_q -N galaxy_stdjob -l > ncpus=1,mem=4gb/' > drmaa_external_killjob_script 'scripts/drmaa_external_killer.py' > drmaa_external_runjob_script 'scripts/drmaa_external_runner.py' > enable_api 'True' > enable_job_recovery 'True' > enable_quotas 'True' > enable_tracks 'False' > environment_setup_file '/g/funcgen/galaxy/env_setup' > error_email_to 'g...@embl.de' > external_chown_script 'scripts/external_chown_script.py' > file_path '/g/galaxy/galaxy_data/files' > here '/g/funcgen/galaxy' > id_secret 'all_your_base_are_belong_to_us' > job_handlers 'runner0' > job_manager 'runner0' > job_working_directory '/g/galaxy/galaxy_data/job_working_directory' > library_import_dir '/home/galaxy/' > log_level 'DEBUG' > logo_url 'http://manni/ngswiki/index.php/Galaxy' > new_file_path '/g/galaxy/galaxy_data/tmp' > nglims_config_file 'tool-data/nglims.yaml' > outputs_to_working_directory 'True' > qa_url 'http://slyfox.bx.psu.edu:8080/' > remote_user_maildomain 'embl.de' > require_login 'True' > retry_job_output_collection '10' > sanitize_all_html 'False' > set_metadata_externally 'True' > smtp_server 'smtp.embl.de' > start_job_runners 'drmaa' > static_cache_time '360' > static_dir '/g/funcgen/galaxy/static/' > static_enabled 'True' > static_favicon_dir '/g/funcgen/galaxy/static/favicon.ico' > static_images_dir '/g/funcgen/galaxy/static/images' > static_robots_txt '/g/funcgen/galaxy/static/robots.txt' > static_scripts_dir '/g/funcgen/galaxy/static/scripts/' > static_style_dir '/g/funcgen/galaxy/static/june_2007_style/blue' > tool_config_file 'tool_conf.xml,shed_tool_conf.xml' > tool_dependency_dir '/g/funcgen/galaxy/dependencies' > tool_path 'tools' > track_jobs_in_database 'True' > use_interactive 'False' > use_nglims 'False' > use_remote_user 'True' > > WSGI Variables > application <paste.debug.prints.PrintDebugMiddleware object at 0x22dbdf90> > paste.cookies (<SimpleCookie: > galaxysession='7df64c2bf0628c5b57afd358adee6e7b2cd6161345bb6b47388e497cbd26f407876c2bed128d9226'wikidb_ngs_Token='1f38fe6b5eb5863596cad189f608835c' > wikidb_ngs_UserID='15' wikidb_ngs_UserName='Girardot' > wikidb_ngs__session='d9n3qq68n0nl6p6j9t96k5q6m3'>, > 'galaxysession=7df64c2bf0628c5b57afd358adee6e7b2cd6161345bb6b47388e497cbd26f407876c2bed128d9226;wikidb_ngs_Token=1f38fe6b5eb5863596cad189f608835c; > wikidb_ngs_UserName=Girardot; wikidb_ngs_UserID=15; > wikidb_ngs__session=d9n3qq68n0nl6p6j9t96k5q6m3') > paste.expected_exceptions [<class 'paste.httpexceptions.HTTPException'>] > paste.httpexceptions <paste.httpexceptions.HTTPExceptionHandler object at > 0x22928b10> > paste.httpserver.thread_pool <paste.httpserver.ThreadPool object at > 0x1ddf9950> > paste.printdebug_listeners [<cStringIO.StringO object at 0x28c57618>, > <paste.script.serve.LazyWriter object at 0x1dd5a6d0>] > paste.recursive.forward <paste.recursive.Forwarder from /galaxy> > paste.recursive.include <paste.recursive.Includer from /galaxy> > paste.recursive.include_app_iter <paste.recursive.IncluderAppIter from > /galaxy> > paste.recursive.script_name '/galaxy' > paste.remove_printdebug <function remove_printdebug at 0x2aaaac032aa0> > paste.throw_errors True > webob._parsed_query_vars (MultiDict([]), '') > wsgi process 'Multithreaded' > > > > ===================================== > Charles Girardot > European Molecular Biology Laboratory > GBCS / Furlong Group > Tel: +49 6221 387 -8585(V205) or -8433 (V320) > Fax: +49-(0)6221-387-8166 > Email: charles.girar...@embl.de > Room V205 (GBCS)/V320 (Furlong Group) > Meyerhofstraße 1, > 69117 Heidelberg, Germany > ===================================== > > > > > > > > > > > > > > ___________________________________________________________ > 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/ ===================================== Charles Girardot European Molecular Biology Laboratory GBCS / Furlong Group Tel: +49 6221 387 -8585(V205) or -8433 (V320) Fax: +49-(0)6221-387-8166 Email: charles.girar...@embl.de Room V205 (GBCS)/V320 (Furlong Group) Meyerhofstraße 1, 69117 Heidelberg, Germany ===================================== ___________________________________________________________ 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/
