You'll probably also want to put that command into a wrapper script
(e.g., shell, make, rake, cap) to make it easier to run, and keep it and
the recipe(s) under revision control.
However, given what you've said, I feel obligated to suggest that you
consider alternative workflows and tools because they may be a better
fit for your situation:
1. Configuration management tools like AutomateIt are ideal for setting
up servers as root. However, if you're using them without root
privileges for some different purpose and have more modest needs, you
may be better off using already-installed tools like bash and Perl, or
maybe use your favorite scripting language.
2. Deployment tools like Capistrano, Vlad the Deployer, Fabric and such
are ideal for deploying custom applications. I typically use AutomateIt
to setup the server (e.g., install Java, and configure and start
Tomcat), but let the developers deploy their custom applications with
their preferred tool (e.g., run an Ant task to upload a .war file and
tell Tomcat to use it; use Capistrano to deploy a Rails app; etc). I
keep server setup and custom application deployment separate because
these tasks are typically done by different people, on different
schedules, and with a strong preference for different tools.
3. If you need to run a stand-alone app without root privileges, tools
like Make, Rake or AutomateIt are good choices for downloading,
compiling and configuring everything so you can get a complete stack
running within your account. However, this is often more time-consuming
and frustrating than setting up a system that you have root on.
Does this answer your questions?
Do you put automateit into a cron job and run it repeatedly? This is
the approach taken by similar software like puppet, chef, cfengine
Personally I can see the need to run some tasks repeatedly but
obviously most things only need to be done once (as long as nobody
comes behind you and undoes them of course).