Error on database_connection statement in universe_wsgi.ini file

7 Aug 2012


      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')
----------------------------

Modification to universe_wsgi.ini file:

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