In eclipse version 4.0 and later versions, most of the ISAAC pipeline is contained in a single Unix command called isaacp. Additional commands are jitter and lwjitter for imaging jitter, they are bound to be included into isaacp sooner or later for consistency.
Once you have compiled isaacp, you can start launching it with no argument to get a list of supported recipes. To get more information about the command itself, try isaacp man. To get more information about one recipe, try isaacp man recipe, where recipe is the name of the recipe you are interested in.