Here’s a simple script to automate mysqlhotcopy runs from cron to backup multiple MySQL databases. The script loops through the list of databases and kicks off an instance of mysqlhotcopy in the background for each one. Really, nothing fancy.

#!/bin/bash
db_user="dbusername"
db_pass="dbuseroass"
backup_dir="/home/databackup/"
if [ -w "${backup_dir}" ]
then
	for db_name in dbname1 dbname2 dbname3
	do
		/usr/bin/mysqlhotcopy -u "${db_user}" -p "${db_pass}" "${db_name}" "${backup_dir}" --allowold --keepold & disown
	done
fi

You can also backup all schemas without specifying their names:

#!/bin/bash
db_user="dbusername"
db_pass="dbuseroass"
backup_dir="/home/databackup/"
MYSQL="/usr/bin/mysql --batch --skip-column-names --max_allowed_packet=100M -u${db_user} -p${db_pass} -e"	
if [ -w "${backup_dir}" ]
then
	for db_name in `$MYSQL "show databases;"`
	do
		/usr/bin/mysqlhotcopy -u "${db_user}" -p "${db_pass}" "${db_name}" "${backup_dir}" --allowold --keepold & disown
	done
fi