Hello, Here's a tip for connecting galaxy to mysql on localhost (if it didn't work for you out of the box): ## Get a clean copy of galaxy $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy ## Create dedicated MySQL database for galaxy, ## with user 'galaxy' and password '12345' $ mysql -u root -p password: mysql> create database galaxy ; mysql> use galaxy ; mysql> grant all on galaxy.* to 'galaxy'@'localhost' identified by '12345'; ## Setup Galaxy $ sh setup.sh ## Change universe_wsgi.ini, to use the new database database_connection = mysql://galaxy:12345@localhost/galaxy ## Run Galaxy $ sh run.sh ----------------- But here's the catch: On a standard debian system, mysql puts the unix socket file in /var/run/mysqld/mysqld.sock However, SqlAlchemy assumes the socket is in /tmp/mysql.sock. So when I run galaxy, I get the following exception: OperationalError: (OperationalError) (2002, "Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)") None None Two possible solutions for that: 1. Change the socket file in /etc/mysql/my.cnf (not recommended) or 2. Add the following incantation to the SQLAlchemy string in universe_wsgi.ini: database_connection = mysql://galaxy:12345@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock With this change, Galaxy runs fine with mysql on localhost. -Gordon.