Hi,
I'm having some problems restarting our galaxy server after upgrading it to the
latest version today...
Here is the error message:
python path is:
/opt/local/home/webapp/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/boto-2.5.2-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/Fabric-1.4.2-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/ssh-1.7.14-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/Whoosh-0.3.18-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/amqplib-0.6.1-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/pexpect-2.4-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/!
Babel-0.9.4-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/Mako-0.4.1-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/WebHelpers-0.2-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/wchartype-0.1-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/elementtree-1.2.6_20050316-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/docutils-0.7-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/WebOb-0.8.5-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/Routes-1.12.3-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/PasteDeploy-1.3.3-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/PasteScript-1.7.3-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/Paste-1.6-py2.7.egg,
/opt/local/home/webapp/galaxy/lib,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/!
setuptools-0.6c11-py2.7.egg, /opt/local/home/webapp/software/p!
ython/py
thon2.7.2/lib/python2.7/site-packages/MySQL_python-1.2.3-py2.7-linux-x86_64.egg,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/termcolor-1.1.0-py2.7.egg,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/PyYAML-3.10-py2.7-linux-x86_64.egg,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/py_mysql2pgsql-0.1.3-py2.7.egg,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg,
/opt/local/home/webapp/software/python/python2.7.2/lib/python27.zip,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/plat-linux2,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-tk,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-old,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-dynload,
/opt/local/home/webapp/softwar!
e/mercurial/mercurial-2.1/lib/python2.7/site-packages,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages
galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,841 Loading
references to tool sheds from tool_sheds_conf.xml
galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,844 Loaded
reference to tool shed: Galaxy main tool shed
galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,844 Loaded
reference to tool shed: Galaxy test tool shed
galaxy.model.migrate.check DEBUG 2012-11-15 14:12:54,884 psycopg2 egg
successfully loaded for postgres dialect
galaxy.model.migrate.check INFO 2012-11-15 14:12:54,975 At database version 107
galaxy.tool_shed.migrate.check DEBUG 2012-11-15 14:12:54,991 psycopg2 egg
successfully loaded for postgres dialect
Traceback (most recent call last):
File "/opt/local/home/webapp/galaxy/lib/galaxy/webapps/galaxy/buildapp.py",
line 36, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/opt/local/home/webapp/galaxy/lib/galaxy/app.py", line 47, in __init__
verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )
File "/opt/local/home/webapp/galaxy/lib/galaxy/tool_shed/migrate/check.py",
line 56, in verify_tools
tool_shed_accessible, missing_tool_configs_dict = check_for_missing_tools(
app, tool_panel_configs, latest_tool_migration_script_number )
File "/opt/local/home/webapp/galaxy/lib/galaxy/tool_shed/migrate/common.py",
line 46, in check_for_missing_tools
tool_dependencies_dict = tool_shed_decode( text )
File "/opt/local/home/webapp/galaxy/lib/galaxy/tool_shed/encoding_util.py",
line 15, in tool_shed_decode
a, b = value.split( ":" )
ValueError: too many values to unpack
Removing PID file paster.pid
Any help would be greatly appreciated. Thanks!
Cheers,
Anne.
--
Anne Pajon, Ph.D. - Bioinformatics Core
Cancer Research UK - Cambridge Institute
Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
anne.pa...@cruk.cam.ac.uk | +44 (0)1223 40 4334
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