I'm certain that the answer is obvious, but I genuinely do not know. I'm on Windows, if that helps. I apologize for asking such a question; I'm a complete neophyte and I've only ever done this when a piece software came with a guide.
You'll need a PC compiler. Assuming you already have devKitPro, install TDM-GCC (make sure you enable the add to path option in the installer),
download the source of Project CTR (which contains makerom and ctrtool) and extract it in (assuming default path) c:/devkitpro/msys/home/yourusername/[Project-CTR/ctrtool/]
Open MSys, the one bundled with devkitpro (not the minGW bundled with TDM!!), enter the folder for ctrtool, and "make" it!