Today I have found a useful texture atlas tool written in C#.
It works like a charm with moon on Linux.
You can download it from http://spritesheetpacker.codeplex.com/ for free and you can get the JSON hash and array exporters from http://www.html5gamedevs.com/topic/2913-texture-atlas-creator/ to get it working with phaser JS.
Follow the instructions in the forum thread to run it!
Source code and instructions in order to build it are available in my github page: https://github.com/gnuton/Playground/tree/master/CSharp/SpriteSheetPacker-JSONArrayExporter