Hi Greg,
Brilliant! Thanks a lot for your advice, it worked!
I do run the latest dist release that went out yesterday. Thanks again for your
prompt help, it is very much appreciated.
Cheers,
Anne.
On 15 Nov 2012, at 16:45, Greg Von Kuster <g...@bx.psu.edu> wrote:
> HI Anne,
>
> Just to confirm, you are running the latest dist release which went out
> yesterday, correct? If so, perhaps you can try this:
>
> %sh manage_tools.sh upgrade
>
> The above will set the value of the migrate_tools.version column in your
> database to the latest migration value. After doing this, try
>
> %sh run.sh
>
> which will start up your Galaxy server. Then you can run any of the tool
> migrations you want by getting the commands from the Admin menu link.
>
> Let me know if this works.
>
> Greg Von Kuster
>
> On Nov 15, 2012, at 11:39 AM, Anne Pajon wrote:
>
>> Hi Greg,
>>
>> No change at all, how can I check?
>>
>> [webapp@uk-cri-lbio07 galaxy]$ hg status | grep -v '^?'
>> M tool-data/shared/ucsc/ucsc_build_sites.txt
>>
>> The problem may be that I did not upgrade since 14 June 2012. Could it be
>> related to the version of tools in the database? Please advice me if you
>> could on the places to look at. I've looked at the code but I did not find
>> yet which data/config file is causing this error.
>>
>> Should I revert the upgrade and try to upgrade to the previous release
>> instead? Any advices would be very much appreciated.
>>
>> Thanks.
>> Cheers,
>> Anne.
>>
>>
>> On 15 Nov 2012, at 16:12, Greg Von Kuster wrote:
>>
>>> 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-pack!
ages/setuptools-0.6c11-py2.7.egg, /opt/local/home/webapp/softw!
are/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/so!
ftware/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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>>
>> --
>> 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.
>>
>
--
Anne Pajon, Ph.D.
Cancer Research UK - Cambridge Research Institute
Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
anne.pa...@cancer.org.uk | +44 (0)7958 511 353
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.
___________________________________________________________
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