You can add a cron job in FASTPANEL. Open the Control section -> Scheduler.
When using ISPmanager: the Main menu -> Scheduler
If you need to run a console script, use the following command:
cd /var/www/USER_NAME/data/www/SITE_NAME/; /usr/bin/php -f cron.php
USER_NAME is the website's owner.
SITE_NAME is the site name.
cron.php - the name of the script to launch.
If you run the script from the browser:
/usr/bin/wget -O /dev/null "http://site.com/cron.php?start=1"
site.com is your site address.
cron.php is your script name.
?start=1 - is a GET request parameter with the value 1 if the script requires specifying these parameters.