Hi Greg,

Database downgrade and then upgrade succeeded! galaxy instance is working now!

many thanks!
michal

On 03/15/2012 08:57 PM, Greg Von Kuster wrote:
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/wcharty!
pe-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-!
packages, /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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--
Michal Stuglik, PhD student
Institute of Environmental Sciences
Molecular and Behavioral Ecology Group
Jagiellonian University
Gronostajowa 7
30-387 Krakow, Poland
www:  http://www.eko.uj.edu.pl/molecol/index.php/zespol/michal-stuglik




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