Nearly all this information was found on the blog: http://aidanjm.wordpress.com/2007/02/15/split-lossless-audio-ape-flac-wv...

The steps below are the steps that I follow to split my own audio that I find still in a single lossless file (usually .wav).

$ sudo apt-get install cuetools shntool flac
$ cuebreakpoints sample.cue | shnsplit -o flac sample.wav
$ cuetag sample.cue split-track*.flac