After some useless search trying to find an SBS TO ANAGLYPH linux software, I realised that what I was looking for was simply a good video editing software under linux. So I started looking for this software, tried several onces and finally found kdenlive (thanks guys this is a really good software)
So for the interested onces here is how to create an anaglyph video from a side by side video (green-magenta in this case but other onces are exactly the same process)
First, start by installing kdenlive, but not any version. If you want to convert from sbs to anaglyph you will need the latest kdenlive version, the reason is double, first we will need the latest features and second we don't want to be annoyed with the early bugs. So i recommend to follow the "install from source" process (quite tricky but necessary):
Once you have a fresh kdenlive version, start by import your sbs video:
Then drag and drop the video on the two first video tracks:
Add a "crop" effect on both tracks and set right parameter to half your video width on the first track and do the same for the left parameter on the other track:
Then add one "levels" effect to the first track, select the green channel and set the "input black level" parameter to 1000. Add two "levels" effect to the second track one for the red channel and the other one for the blue channel, again set the "input black level" parameter to 1000 for both effects:
Finaly, right click on the first track and go to "add transition/addition", then stretch the effect to the complete track:
Here it is, SBS to anaglyph conversion in 5 steps. Now render your video (I usually render without audio and recombine audio and video using MKVmerge).
For other anaglyphs you will probably only have to play with the "levels" effects.