We have a whenever cookbook in our repo we use that you would be more than welcome to use here: https://github.com/freerunningtech/frt-opsworks-cookbooks. I assume you're familiar with adding custom cookbooks to your opsworks stacks.
We generally run it on its own layer that also includes the rails cookbooks required for application deployment (while not the app server):
- Configure: rails::configure
- Deploy: deploy::rails whenever
- Undeploy: deploy::rails-undeploy
However, we usually also deploy this instance as an application server, meaning we do end up serving requests from the box we're using for whenever as well.
There is one "gotcha", in that you must set your path in the env at the top of the schedule.rb like this:
env :PATH, ENV['PATH']