For starts, you have to give us a bit more information. You said you are "creating a version of moodle" which is confusing. I suppose it is possible that you are rewriting moodle, but you've got a very long road ahead of you if you want to do that.
If on the other hand you mean you intend to install (or create an "instance" ) of moodle, then that's a different story. Even so, the question still doesn't make much sense. Moodle is written in PHP - so it needs PHP enabled on your webserver, and you actually would install the PHP code that makes up Moodle. You can do this by checking out the documentation first, http://moodle.org/mod/resource/view.php?id=3856 and then downloading http://download.moodle.org/?lang=en and installing it according to the instructions.
As far as writing additional code, you could do it in java I suppose but that wouldn't make much sense since it's all in PHP, and the decent thing to do if you customize anything would be to share your customizations with the moodle community.
Lastly, it sounds like you might want installation help, but you've posted this question to the documentation course whereas you might get better results and more relevant audiences by posting a more specific question to a forum within the USING MOODLE course, like that for installation problems: http://moodle.org/mod/forum/view.php?id=28
Regards, and welcome to the community.