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/wchartype!
-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-pa!
ckages, /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
___________________________________________________________
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