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')
----------------------------
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___________________________________________________________
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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
