Bonjour a tous,

Je suis pas sur que soumettre ce probleme a la communaute francaise soit plus efficace que de le faire avec la communaute anglaise mais travaillant 100% en environnement anglais ca fait du bieb de pouvoir s'exprimer sur son travail en francais.

Je suis responsable d'un pilote galaxy de production, le serveur abrite une version de production et une version de developpement. Je suis dependant des ITs pour une partie de la maiNtenance de ces serveurs (et oui je ne suis qu'un faible biologiste trempant ses mains dans le cambouis de la bioinformatique). Pour divers raisons techniques j'ai egalement installer une version locale sur mon propre ordinateur afin de pouvoir jouer aveca volonte. J'ai pas de probleme pour installer differents outils venant du toolshed (enfin si mais rien d'insurmontable). J'essaye actuellement d'installer une version locale du toolshed et j'ai vraiment du mal avec ca, j'ia essaye de suivre les informations trouvees ici http://wiki.g2.bx.psu.edu/HostingALocalToolShed#Hosting_your_own_local_tool_... et la http://www.agapow.net/science/bioinformatics/galaxy/setting-up-a-galaxy-tool... mais certaines choses m'echappent et il ne se passe rien qund je lance le script de demarrage du toolshe, ou plutot le processus est tue en raison d'une erreur que je ne comprends pas. Voir ci dessous. Est ce que certain d'entre vous pourrez partager leur experience a ce sujet et eventuellemt m'indiquer ou chercher pour regler ce probleme.

Merci d'avance. Philippe

###############community_webapp.log /home/mon13m/Galaxy-local/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/lib/python2.7/dist-packages/markupsafe/__init__.pyc, but /home/mon13m/Galaxy-local/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict() python path is: /home/mon13m/Galaxy-local/galaxy-dist/eggs/Fabric-1.4.2-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/ssh-1.7.14-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/Whoosh-0.3.18-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs4.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs4.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs4.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/amqplib-0.6.1-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/pexpect-2.4-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/WebHelpers-0.2-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs4.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/wchartype-0.1-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/eggs/Paste-1.6-py2.7.egg, /home/mon13m/Galaxy-local/galaxy-dist/lib, /usr/lib/python2.7, /usr/lib/python2.7/plat-linux2, /usr/lib/python2.7/lib-tk, /usr/lib/python2.7/lib-old, /usr/lib/python2.7/lib-dynload, /usr/local/lib/python2.7/dist-packages, /usr/lib/python2.7/dist-packages/PIL, /usr/lib/python2.7/dist-packages/gst-0.10, /usr/lib/python2.7/dist-packages/gtk-2.0, /usr/lib/pymodules/python2.7, /usr/lib/python2.7/dist-packages/ubuntu-sso-client, /usr/lib/python2.7/dist-packages/ubuntuone-client, /usr/lib/python2.7/dist-packages/ubuntuone-control-panel, /usr/lib/python2.7/dist-packages/ubuntuone-couch, /usr/lib/python2.7/dist-packages/ubuntuone-installer, /usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol, /usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode, /usr/lib/python2.7/dist-packages galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,937 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,944 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,944 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,944 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,944 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,944 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,944 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,944 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,944 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,944 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,944 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,944 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,945 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,945 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,945 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,945 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,945 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,945 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,945 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,945 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,945 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,945 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,945 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,945 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,945 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,946 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,946 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,946 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,946 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,946 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,946 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,946 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,946 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,946 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,946 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,946 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,946 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,946 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,947 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,947 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,947 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2012-10-15 15:46:23,947 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.webapps.community.model.migrate.check DEBUG 2012-10-15 15:46:23,969 psycopg2 egg successfully loaded for postgres dialect Traceback (most recent call last): File "/home/mon13m/Galaxy-local/galaxy-dist/lib/galaxy/webapps/community/buildapp.py", line 69, in app_factory app = UniverseApplication( global_conf=global_conf, **kwargs ) File "/home/mon13m/Galaxy-local/galaxy-dist/lib/galaxy/webapps/community/app.py", line 29, in __init__ create_or_verify_database( db_url, self.config.database_engine_options ) File "/home/mon13m/Galaxy-local/galaxy-dist/lib/galaxy/webapps/community/model/migrate/check.py", line 48, in create_or_verify_database engine = create_engine( url, **engine_options ) File "/home/mon13m/Galaxy-local/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/__init__.py", line 223, in create_engine return strategy.create(*args, **kwargs) File "/home/mon13m/Galaxy-local/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/strategies.py", line 46, in create u = url.make_url(name_or_url) File "/home/mon13m/Galaxy-local/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/url.py", line 137, in make_url return _parse_rfc1738_args(name_or_url) File "/home/mon13m/Galaxy-local/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/url.py", line 173, in _parse_rfc1738_args return URL(name, **components) File "/home/mon13m/Galaxy-local/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/url.py", line 49, in __init__ self.port = int(port) ValueError: invalid literal for int() with base 10: '' Removing PID file community_webapp.pid

##############community_wsgi.ini # ---- HTTP Server ----------------------------------------------------------

[server:main]

use = egg:Paste#http port = 9009

# The address on which to listen. By default, only listen to localhost (the tool shed will not # be accessible over the network). Use '0.0.0.0' to listen on all available network interfaces. #host = 0.0.0.0 host = 127.0.0.1

use_threadpool = true threadpool_workers = 10

[filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /toolshed

# ---- Galaxy Webapps Community Interface -------------------------------------------------

[app:main]

filter-with = proxy-prefix cookie_path = /toolshed

# Specifies the factory for the universe WSGI application paste.app_factory = galaxy.webapps.community.buildapp:app_factory log_level = DEBUG

# Database connection database_file = /home/mon13m/Galaxy-local/galaxy-dist/database/community.sqlite # You may use a SQLAlchemy connection string to specify an external database instead #database_connection = postgres:///community_test?host=/var/run/postgresql database_connection = postgres://galaxy:password@http:/127.0.0.1:9009/galaxy_toolshed

# Where dataset files are saved file_path = /home/mon13m/Galaxy-local/galaxy-dist/database/community_files # Temporary storage for additional datasets, this should be shared through the cluster new_file_path = /home/mon13m/Galaxy-local/galaxy-dist/database/tmp

# Session support (beaker) use_beaker_session = True session_type = memory session_data_dir = %(here)s/database/beaker_sessions session_key = galaxysessions session_secret = changethisinproduction

# Galaxy session security id_secret = changethisinproductiontoo

# Configuration for debugging middleware debug = true use_lint = false

# NEVER enable this on a public site (even test or QA) # use_interactive = true

# this should be a comma-separated list of valid Galaxy users # admin_users =

# Force everyone to log in (disable anonymous access) require_login = False

# path to sendmail sendmail_path = /usr/sbin/sendmail

# For use by email messages sent from the tool shed #smtp_server = smtp.your_tool_shed_server #email_from = your_tool_shed_email@server

# The URL linked by the "Support" link in the "Help" menu. #support_url = http://wiki.g2.bx.psu.edu/Support

# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) ## use_heartbeat = True

# Profiling middleware (cProfile based) ## use_profile = True

# Use the new iframe / javascript based layout use_new_layout = true

# Serving static files (needed if running standalone) static_enabled = True static_cache_time = 360 static_dir = %(here)s/static/ static_images_dir = %(here)s/static/images static_favicon_dir = %(here)s/static/favicon.ico static_scripts_dir = %(here)s/static/scripts/ static_style_dir = %(here)s/static/june_2007_style/blue