Yes that worked! Thanks,
Liisa




From:   Jeremy Goecks <jeremy.goe...@emory.edu>
To:     Liisa Koski <liisa.ko...@basf.com>
Cc:     <galaxy-dev@lists.bx.psu.edu>
Date:   23/01/2013 11:02 PM
Subject:        Re: [galaxy-dev] Fw: Error when attempting to install new 
distributuion - TypeError: Invalid argument(s) 'server_side_cursors', 
'max_overflow'



My guess is that you'll need to comment out some database options in your 
universe_wsgi.ini file that are valid for MySQL but not for SQLite. 
Specifically, database_engine_option_max_overflow and perhaps other 
options as well.

Best,
J.

On Jan 23, 2013, at 1:54 PM, Liisa Koski wrote:

Hello, 
I am attempting to install a new galaxy-dist and am running into the 
following error. I first tried it by using a mysql database but this error 
also occurs when I use the default SQLite database. 
Any help would be much appreciated. 
Thanks in advance, 
Liisa 

[galaxy-dev]$ ./run.sh 
Some eggs are out of date, attempting to fetch... 
Fetched 
http://eggs.galaxyproject.org/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.6-linux-x86_64-ucs4.egg
 

Fetch successful. 
galaxy-dev/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: galaxy-dev/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, 
galaxy-dev/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, 
galaxy-dev/eggs/boto-2.5.2-py2.6.egg, 
galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg, 
galaxy-dev/eggs/Fabric-1.4.2-py2.6.egg, 
galaxy-dev/eggs/ssh-1.7.14-py2.6.egg, 
galaxy-dev/eggs/Whoosh-0.3.18-py2.6.egg, 
galaxy-dev/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, 
galaxy-dev/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, 
galaxy-dev/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, 
galaxy-dev/eggs/amqplib-0.6.1-py2.6.egg, 
galaxy-dev/eggs/pexpect-2.4-py2.6.egg, 
galaxy-dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, 
galaxy-dev/eggs/Babel-0.9.4-py2.6.egg, 
galaxy-dev/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, 
galaxy-dev/eggs/Mako-0.4.1-py2.6.egg, 
galaxy-dev/eggs/WebHelpers-0.2-py2.6.egg, 
galaxy-dev/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, 
galaxy-dev/eggs/wchartype-0.1-py2.6.egg, 
galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg, 
galaxy-dev/eggs/docutils-0.7-py2.6.egg, 
galaxy-dev/eggs/WebOb-0.8.5-py2.6.egg, 
galaxy-dev/eggs/Routes-1.12.3-py2.6.egg, 
galaxy-dev/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, 
galaxy-dev/eggs/PasteDeploy-1.3.3-py2.6.egg, 
galaxy-dev/eggs/PasteScript-1.7.3-py2.6.egg, 
galaxy-dev/eggs/Paste-1.6-py2.6.egg, galaxy-dev/lib, 
/usr/lib64/python2.6/site-packages/distribute-0.6.12-py2.6.egg, 
/usr/lib64/python2.6/site-packages/blist-1.3.4-py2.6-linux-x86_64.egg, 
/usr/lib/python2.6/site-packages/nose-1.0.0-py2.6.egg, 
/usr/lib/python2.6/site-packages/argparse-1.2.1-py2.6.egg, 
/usr/lib/python2.6/site-packages/pip-1.2.1-py2.6.egg, 
/usr/lib/python2.6/site-packages, /usr/lib64/python2.6/xml/etree, 
/usr/lib64/python26.zip, /usr/lib64/python2.6, 
/usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk, 
/usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload, 
/usr/lib64/python2.6/site-packages/PIL, 
/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg-info, 
/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg-info, 
/usr/lib64/python2.6/site-packages 
galaxy.tool_shed.tool_shed_registry DEBUG 2013-01-21 13:52:06,034 Loading 
references to tool sheds from tool_sheds_conf.xml 
galaxy.tool_shed.tool_shed_registry DEBUG 2013-01-21 13:52:06,034 Loaded 
reference to tool shed: Galaxy main tool shed 
galaxy.tool_shed.tool_shed_registry DEBUG 2013-01-21 13:52:06,034 Loaded 
reference to tool shed: Galaxy test tool shed 
galaxy.model.migrate.check DEBUG 2013-01-21 13:52:06,112 pysqlite>=2 egg 
successfully loaded for sqlite dialect 
Traceback (most recent call last): 
  File "galaxy-dev/lib/galaxy/webapps/galaxy/buildapp.py", line 36, in 
app_factory 
    app = UniverseApplication( global_conf = global_conf, **kwargs ) 
  File "galaxy-dev/lib/galaxy/app.py", line 45, in __init__ 
    create_or_verify_database( db_url, kwargs.get( 'global_conf', {} 
).get( '__file__', None ), self.config.database_engine_options, app=self ) 

  File "galaxy-dev/lib/galaxy/model/migrate/check.py", line 46, in 
create_or_verify_database 
    engine = create_engine( url, **engine_options ) 
  File 
"galaxy-dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/__init__.py",
 
line 223, in create_engine 
    return strategy.create(*args, **kwargs) 
  File 
"galaxy-dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/strategies.py",
 
line 121, in create 
    engineclass.__name__)) 
TypeError: Invalid argument(s) 'server_side_cursors','max_overflow' sent 
to create_engine(), using configuration 
SQLiteDialect/SingletonThreadPool/TLEngine.  Please check that the keyword 
arguments are appropriate for this combination of components.
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