Cannot create a mysql database

Credentials problem:

To install SMRT Portal, you must know the credentials to log into your mysql server as root. The configure_smrtanalysis.sh script will prompt you for the username (default root) and the password (default no password).

You can test different passwords to see if you can log by typing the following:

mysql -u <root> -p <mysql>

If you do not know your password or your system administrator has forgotten it, you may want to try resetting it like so: http://dev.mysql.com/doc/refman/5.0/en/resetting-permissions.html

Bind address problem:

SMRT Portal has difficulty connecting to the smrtportal mysql database after installation if you have a unique setting in your myslq my.conf file. A typical error when you try to create the first administrator user is

Error listing Users. Case; 'hibernate.dialect' must be set when no Connection available.

Check that you are using a different bind address: grep bind /etc/mysql/my.cnf

If you had changed the bind address to something other than the default 127.0.0.1, then you need to replace localhost in the $SEYMOUR_HOME/redist/tomcat/webapps/smrtportal/WEBINF/classes/META-INF/persistence.xml file with the actual IP address, or hostname of the server running mysql.