how do I convert an animated gif to a video (e.g. h264@mp4) programmatically on a linux server?
I need this to process user generated content which should be output
ffmpeg has better GIF demuxing support (and improved GIF encoding). I recommend ditching avconv and getting ffmpeg (the real one from FFmpeg; not the old charlatan from Libav). A static build is easy, or you can of course compile.
ffmpeg -i in.gif -c:v libx264 -pix_fmt yuv420p -movflags +faststart out.mp4
See the FFmpeg Wiki: H.264 Encoding Guide for more examples.