ffmepg is a integrated tool for video encoding/decoding processing as open source project - http://ffmpeg.org
You can easily convert video file to mp4 like below simple command on your linux device.
ffmpeg –i source_video.mov –vcodec h264 –acodec mp2 my-video.mp4
If you want to use audio codec by aac in the video, it will be super simple like:
ffmpeg –i source_video.mov –vcodec h264 –acodec aac my-video.mp4