maybe you need to include username, password and host? database_connection = mysql://<username>:<password>@<host>/<database>?unix_socket=/var/run/mysqld/mysqld.sock Regards, Hans On 08/07/2012 03:19 AM, Kenneth Auerbach wrote:

Hello,

Galaxy runs fine 'out of the box' with the default universe_wsgi.ini initialization file. But when I change the "database_connection" statement to connect to my MySql database, I get the errors below. Can you please tell what the problem is? Thanks!

-Wolf.

Modification to universe_wsgi.ini file: ------------------------------------ #database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE

database_connection = mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock -------------------------------------

Then when I type "sh run.sh" I get this:

--------- wolf@linuxmint ~/Downloads/galaxy-galaxy-dist-ec29ce8e27a1 $ sh run.sh Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run result = self.command() File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 313, in loadapp **kw) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 413, in get_context section) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 458, in _context_from_explicit value = import_string(found_expr) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 18, in import_string return pkg_resources.EntryPoint.parse("x="+s).load(False) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/lib/pkg_resources.py", line 1997, in parse src ValueError: ("EntryPoint must be in 'name=module:attrs [extras]' format", 'x=galaxy.web.buildapp:app_factory\ndatabase_connection = mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock') ---------------------------- ___________________________________________________________ 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/