ffmpeg -i source.mov -f mp4 -vcodec copy -acodec copy output.mp4
Unfortunately Ubuntu 14.04 does not have FFmpeg at all in the standard repositories, an issue that has been rectified in subsequent Ubuntu releases. If you are keen to use default 14.04 offerings you would be using avconv from libav-tools. Use the following:
sudo apt-get install libav-tools libavcodec-extra-54
And then to simply change containers from mov to mp4:
avconv -i input.mov -codec copy output.mp4
If you would prefer a modern version of FFmpeg that fits in well with Trusty Tahr 14.04 (and I would recommend this path) there are 2 good choices:
Use Doug McMahon's great Trusty Multimedia PPA
Compile your own bleeding edge FFmpeg from FFmpeg trac instructions
Lots of good choices! For FFmpeg the command line is only slightly different:
ffmpeg -i input.mov -codec copy output.mp4
And that should solve your issue...
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