I figured out out to get Java Tomcat 6.0.18 and mysql connector j 5.1.7.

I shutdown tomcat and put the mysql j connector jar in the apache-tomcat-6.0.18/lib folder

I edited /etc/my.cnf to set the bind address to 127.0.0.1 and commented out skip networking now it works

I was giving pool resources errors before that or nested sql exception. you can test if this is an issue with I think

mysql -h 127.0.0.1 -u root -p

Now i can run my java programs that require mysql