[Galaxy-france] Installation d'une version locale du toolshed

classic Classique list Liste threaded Arborescence
1 message Options
| Arborescence
Ouvrir ce message en vue arborescente
|

[Galaxy-france] Installation d'une version locale du toolshed

Moncuquet, Philippe (CMIS, Acton)
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_shed
et la
http://www.agapow.net/science/bioinformatics/galaxy/setting-up-a-galaxy-toolshed
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 = [hidden email]



# 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

_______________________________________________
Galaxy-France mailing list
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-france