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 'girardot@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 'su@embl.de,sauer@embl.de,girardot@embl.de,galaxy@embl.de' allow_library_path_paste 'True' allow_user_dataset_purge 'True' allow_user_impersonation 'True' api_allow_run_as 'galaxy@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 'gbcs@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.girardot@embl.de Room V205 (GBCS)/V320 (Furlong Group) Meyerhofstraße 1, 69117 Heidelberg, Germany =====================================