Install required libs (this was done on a mac).

brew install cuetools flac ffmpeg shntool

Split the file
shnsplit -o flac -f file.cue file.flac

Links:
https://coderwall.com/p/6ydyoq/how-to-split-flac-files-by-cue-and-convert-to-alac-on-mac-os-x

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