On my current project I make all my Clojure files resources, load them, and call the functions directly. The following example shows Clojure printing the argument it's given.
(defn print-string [arg]
// Java calling code
RT.var("printer", "print-string").invoke("hello world");
There's a few things worth noting about the example: RT.var takes the namespace name and the function name. The Var returned by RT.var has an
invokemethod that allows you to pass any number of Objects. The
invokemethod also returns an Object, which allows you return values from Clojure where necessary.
It's also worth noting that the Clojure/Java interop is very, very good. You could pass a Java object to Clojure, make changes to it in Clojure, and return it back to Java. Of course, you might not even need to return it to Java since the instance referenced in Clojure would be the same instance referenced in Java.