running parallel workflow fails

16 Jan 2013

      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
=====================================

Charles Girardot

Charles Girardot

tags

participants (1)