Native flac .cue splitter

First you need to install cuetools and shntool. From the terminal type:

sudo apt install cuetools shntool flac

To split a flac file back to the original files using a .cue file:

cuebreakpoints '<cue file>' | shnsplit -o flac '<audio flac file>'  

You can drag the cue file and the audio flac file from the file manager into the terminal in order to autocomplete the paths for '<cue file>' and '<audio flac file>'. When you run the command, the terminal will show you the results of each new flac file as it is created, one new flac file at a time ("split-track01.flac" "split-track02.flac" ...), and then stop after all of the new flac files have been created. It only takes a few seconds to create each new flac file. If your .cue file is accurate, the results will be more accurate and less time-consuming than if you split the flac file manually in Audacity.

There is a app called Flacon which does exactly this.

To install:

sudo add-apt-repository ppa:flacon
sudo apt-get update
sudo apt-get install flacon

I needed to split large flac and set file name and tag from the cue file, and this worked best for me:

1. cd to a folder with one pair of cue and flac
2. type this: shnsplit -f *.cue -t "%n - %p - %t" -o "flac flac -s -8 -o %f -" *.flac
3. delete the original flac file
4. tag the files using: cuetag *.cue *.flac

Example of output:

Splitting [Edvard Grieg - Complete Songs Vol.III.flac] (76:03.40) --> [25 - Edvard Grieg - Sighs, EG 134.flac] (2:43.08) : 100% OK

reference: CUE_Splitting

UPDATE

I wrote the following script for my convenience. To use it - cd to a directory with one pair of matching ape and cue files.

mkdir -p orig
mv *ape orig/.
shnsplit -f *.cue -t "%n - %p - %t" -o "flac flac -s -8 -o %f -" orig/*.ape
rm -f 00*
cuetag *.cue *.flac
#fix bad file names
find . -exec rename 's/[^\x00-\x7F]//g' "{}" \;

name this script as split_ape, chmod +x it and put in some directory in your path. I made a similar script for flac file as source, just replace every ape with flac in this script.