I upgraded from Yosemite to El Capitan. MySQL needs to be upgraded to at least 5.7.9. This version corrects previous issues with starting mysql on boot as Apple changed the launch process on OSX Yosemite onwards. At the time of this article the current version is 5.7.10, download it from http://dev.mysql.com/downloads/mysql/ and choose the DMG version.
Run through the install. The guide here http://coolestguidesontheplanet.com/get-apache-mysql-php-and-phpmyadmin-working-on-osx-10-11-el-capitan/ is a good one.
After you do this you may be one of the unfortunate ones to have the error display “ERROR! The server quit without updating PID file”. It took me awhile to find the solution which is posted http://stackoverflow.com/questions/33225652/mysql-error-on-el-capitan-os-after-yosemite-os-update
However, when I ran
ps -ax | grep mysql
I had 2 –pid-file. I choose the one that looked like a default and completed the steps. Edit /private/etc/my.cnf and at the end of the file put
pid-file = /path/to/your/local/mysqld.local.pid
You may also want to update your /private/etc/my.cnf file in order to do larger database imports. I published my file and you can read about it here.