Hi Freerk,
When we change the databaseconnection to "mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock" in the universe_wsgi.ini file and run Galaxy we receive an error like:
"Access denied for user 'root'@'localhost' (using password: NO)") None None
So is there an option somewhere which we also have to change to make the connection work?
You need to specify a username and password to access your database. Try this URL: mysql://user:password@localhost/galaxy?unix_socket=/var/lib/mysql/mysql.sock (exchanging 'user' and 'password' according to your settings)
And question two: Do we need to migrate the content from the sqlite database to the MySQL database by hand or does this happen automatically?
You need to do the migration manually. Kanwei provided a nice solution to this problem a while back: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-February/001996.html -- What I would suggest is to dump the sqlite database to standard sql, and then creating a new instance of galaxy that has mysql as the configured database. When you run the setup and run script, you'll have a freshly instantiated galaxy with empty mysql tables. Then you can just import the standard sql file into the mysql database. -- Good luck and let us know if you have any more problems. J.