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/egg!
 s/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-package!
 s/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/softw!
 are/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
> 
> 
> NOTICE AND DISCLAIMER
> This e-mail (including any attachments) is intended for the above-named 
> person(s). If you are not the intended recipient, notify the sender 
> immediately, delete this email from your system and do not disclose or use 
> for any purpose. 
> 
> We may monitor all incoming and outgoing emails in line with current 
> legislation. We have taken steps to ensure that this email and attachments 
> are free from any virus, but it remains your responsibility to ensure that 
> viruses do not adversely affect you. 
> Cancer Research UK
> Registered charity in England and Wales (1089464), Scotland (SC041666) and 
> the Isle of Man (1103)
> A company limited by guarantee.  Registered company in England and Wales 
> (4325234) and the Isle of Man (5713F).
> Registered Office Address: Angel Building, 407 St John Street, London EC1V 
> 4AD.
> 
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to