Hi Anne, We've never seen this error before and we are not able to reproduce it, so not sure we can help. Have you made any changes to your Galaxy code base or to your Galaxy environment? Greg Von Kuster On Nov 15, 2012, at 9:15 AM, Anne Pajon wrote:
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/software/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.pajon@cruk.cam.ac.uk | +44 (0)1223 40 4334
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