Yes that worked! Thanks, Liisa From: Jeremy Goecks <jeremy.goecks@emory.edu> To: Liisa Koski <liisa.koski@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 Thanks in advance, Liisa [galaxy-dev]$ ./run.sh Some eggs are out of date, attempting to fetch...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-li... 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. ___________________________________________________________ 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/