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













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