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/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-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 ___________________________________________________________ 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: