Put your command in a text file, such as runupdate.sql
Then your cron command will be something like this:
mysql -uYOURUSER -pYOURPASSWORD < /full/path/runupdate.sql
This page might be helpful, and shows how to do the same thing as the "<" but using command line switches: [dev.mysql.com...]
The above assumes that the MySQL Command Line Client is installed on your server. I don't know if that is the usual case on shared hosting servers, but it might be.
If you get an error that the mysql program doesn't exist on the server, you could put your command in a .php script (along with the necessary connection code, etc.) and run that from cron. I'm less sure of the cron syntax for that, but it might be something like
If I'm on the right track, I'm hoping others can fill in needed details or correct errors.