cron jobs via aws opsworks

I'm migrating off java web app from GAE to AWS, I have a dozen cron jobs each has a different schedule (one of them has a different timezone), it was quite an easy task @ gae, just appending the servlet & time to execute to the cron.xml file.

I know how to set cron job on linux but I'm guessing aws OpsWorks is better suited for this task, how do I attach a java program to OpsWorks ? I haven't seen any way to run a command (I used Jenkins)