For us Linuxians, ffmpeg is the way to go
(fuck avconv/libav, those guys are traitors and poisoned Debian with their unholy fork)
But bear in mind three things:
1) Support for TAK was added not that long ago (IIRC, it was merged somewhere around last year), so make sure to use a up-to-date binary. Or even better - if you do Linux, build your own from scratch and screw whatever crippled/outdated garbage your distro ships.
2) Decoding might be slow, dunno how optimized is the ffmpeg TAK decoder
3) Things like embedded CUEsheets are a pain for transfering (at least ffmpeg will print it to stdout, but then have fun copying that from a console - if your shell-fu is awesome-ninja-enough, well, you might devise a method for taking that embedded CUE and splitting and stuff), and you might even lose some metadata. Be careful with that.