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)
> Meyerhofstra├če 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)
Meyerhofstra├če 1, 
69117 Heidelberg, Germany
=====================================













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