The correct process depends a lot on your environment. I work on deployment systems for complex web/mobile infrastructure with many long running Clojure processes. For this we use Pallet to create instances with the code checked out and configured, then we have a function that generates init scripts to start the services at boot. This process is appropriate to environments where you need a repeatable build on a cloud provider so it may be too heavy for your situation.
If you are looking for simple recurring jobs you may want to look into Immutant which is an application server for Clojure with good support for recurring jobs.