Hi Michel,

No idea why, but for some reason your database migration script number 92 
failed.  You should try the following from your Galaxy installation directory:

%sh manage_db.sh downgrade 91

and then:

%sh manage_db.sh upgrade

If this succeeds, try starting Galaxy.  If Galaxy starts, great - all is good!

If you see the same problem you reported below, try running this sql statement 
in your psotgres database:

INSERT INTO migrate_tools VALUES ('GalaxyTools', 
'lib/galaxy/tool_shed/migrate', 1);

Now start your Galaxy server.

Let me know how this turns out.

Greg Von Kuster


On Mar 15, 2012, at 3:40 PM, Michal Stuglik wrote:

> 
> Hi Greg,
> 
> migrate_tools table is empty. Any idea?
> 
> 
> best,
> michal
> 
> 
> 
> W dniu 2012-03-14 18:14, Greg Von Kuster pisze:
>> Hi Michal,
>> 
>> Looks like you're running with a postgres database - can you get into your 
>> database and execute the following sql command and send me the result?
>> 
>> select * from migrate_tools;
>> 
>> Thanks!
>> 
>> Greg Von Kuster
>> 
>> 
>> On Mar 14, 2012, at 12:04 PM, Michal Stuglik wrote:
>> 
>>> Dear galaxy,
>>> 
>>> I have upgraded my galaxy-dist with last official version (  upgrade: % hg 
>>> pull -u -r 40f1816d6857 ). I also upgraded database (sh manage_db.sh 
>>> upgrade).
>>> 
>>> now I have problem with running galaxy instance and this is what I get:
>>> 
>>> 
>>> /home/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
>>>  RuntimeWarning: __builtin__.file size changed, may indicate binary 
>>> incompatibility
>>>  from csamtools import *
>>> python path is: 
>>> /home/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, 
>>> /home/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
>>>  /home/galaxy/galaxy-dist/eggs/boto-2.2.2-py2.6.egg, 
>>> /home/galaxy/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg, 
>>> /home/galaxy/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg, 
>>> /home/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
>>>  
>>> /home/galaxy/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
>>>  /home/galaxy/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, 
>>> /home/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, 
>>> /home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, 
>>> /home/galaxy/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, 
>>> /home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, 
>>> /home/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, 
>>> /home/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, 
>>> /home/galaxy/galaxy-dist/eggs/wchartyp!
 e-0.1-py2.6.egg, 
/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, 
/home/galaxy/galaxy-dist/eggs/docutils-0.7-py2.6.egg, 
/home/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, 
/home/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, 
/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, 
/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, 
/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, 
/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg, 
/home/galaxy/galaxy-dist/lib, /usr/lib/python2.6, 
/usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk, 
/usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload, 
/usr/local/lib/python2.6/dist-packages, /usr/lib/python2.6/dist-packages/PIL, 
/usr/lib/pymodules/python2.6/gtk-2.0, 
/usr/lib/python2.6/dist-packages/gst-0.10, 
/usr/lib/python2.6/dist-packages/gtk-2.0, 
/usr/lib/pymodules/python2.6/ubuntuone-storage-protocol, 
/usr/lib/pymodules/python2.6/ubuntuone-client, /usr/lib/python2.6/dist-p!
 ackages, /usr/lib/pymodules/python2.6
>>> galaxy.model.migrate.check DEBUG 2012-03-14 16:29:23,928 psycopg2 egg 
>>> successfully loaded for postgres dialect
>>> galaxy.model.migrate.check INFO 2012-03-14 16:29:24,000 At database version 
>>> 93
>>> galaxy.tool_shed.migrate.check DEBUG 2012-03-14 16:29:24,007 psycopg2 egg 
>>> successfully loaded for postgres dialect
>>> Traceback (most recent call last):
>>>  File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in 
>>> app_factory
>>>    app = UniverseApplication( global_conf = global_conf, **kwargs )
>>>  File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 37, in __init__
>>>    verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( 
>>> '__file__', None ), self.config.database_engine_options )
>>>  File "/home/galaxy/galaxy-dist/lib/galaxy/tool_shed/migrate/check.py", 
>>> line 42, in verify_tools
>>>    db_schema = schema.ControlledSchema( engine, migrate_repository )
>>>  File 
>>> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
>>>  line 24, in __init__
>>>    self._load()
>>>  File 
>>> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
>>>  line 42, in _load
>>>    data = list(result)[0]
>>> IndexError: list index out of range
>>> 
>>> 
>>> best,
>>> michal
>>> ___________________________________________________________
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> 
> 
> 


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