If you have something like:
define(['dep1', 'dep2', 'dep3'], function (dep1, dep2, dep3) {
var module = {
...
};
return module;
});
change it to:
define(['dep1', 'dep2', 'dep3'], function (dep1, dep2, dep3) {
var module = {
...
};
var init = function (options) {
// Initialize here
return module;
};
return init;
});
Then after requiring your module somewhere, you can call it to initialize. You might also want to look into the factory pattern if you need something more complex and return the factory.
require.js does not restrict you in what you return. It can be a simple object, a string, a function...