making a program run at startup with cmd

Open Terminal (but dont type anything in the window)
Go File > Save
Make your window look like this:

Click Save
Then open up system prefrences and go to Accounts.
Click the name of your account
Click on the Login Items tab
Click the Plus and add in Terminal. Then click the check box next to it (This will make it run but not pop up a terminal window)

 

If you wanted to make it start up at boot-up then you would need to enter that into the cron tab as i recall. I don't know how to do this but i will take a look.

 

cron is for recurring tasks. if you want to make it start at boot, you put it one of the "/etc/rc" scripts.

 

I see. mc86k would know how to set this up. As he wrote a script for folding that starts folding on boot up.