apt-cache show shntool
shntool has native support for .wav files. If you want it to work with
other formats, you must have the appropriate helper program installed.
man shnsplit
The following formats are currently supported:
wav RIFF WAVE file format
aiff Audio Interchange File Format (AIFF and uncompressed/sowt AIFF-C only) (via 'sox'):
<http://sox.sourceforge.net/>
shn Shorten low complexity waveform coder (via 'shorten'):
<http://www.softsound.com/Shorten.html>
<http://www.etree.org/shnutils/shorten/>
flac Free Lossless Audio Codec (via 'flac'):
<http://flac.sourceforge.net/>
ape Monkey's Audio Compressor (via 'mac'):
<http://www.monkeysaudio.com/>
<http://supermmx.org/linux/mac/>
ofr OptimFROG Lossless WAVE Audio Coder (via 'ofr'):
<http://www.losslessaudio.org/>
lpac Lossless Predictive Audio Compression (via 'lpac'):
<http://www.nue.tu-berlin.de/wer/liebchen/lpac.html>
wv WavPack Hybrid Lossless Audio Compression (via 'wavpack' and 'wvunpack'):
<http://www.wavpack.com/>
alac Apple Lossless Audio Codec (via 'alac'):
<http://craz.net/programs/itunes/alac.html>
la Lossless Audio (via 'la'):
<http://www.lossless-audio.com/>
tta TTA Lossless Audio Codec (via 'ttaenc'):
<http://tta.sourceforge.net/>
als MPEG-4 Audio Lossless Coding (via 'mp4als'):
<http://www.nue.tu-berlin.de/forschung/projekte/ ‐
lossless/mp4als.html>
tak (T)om's lossless (A)udio (K)ompressor (via 'takc'):
<http://www.thbeck.de/Tak/Tak.html>
bonk Bonk lossy/lossless audio compressor (via 'bonk'):
<http://www.logarithmic.net/pfh/bonk>
kxs Kexis lossless WAV file compressor (via 'kexis'):
<http://www.sourceforge.net/projects/kexis/>
mkw MKW Audio Compression format (via 'mkwcon'):
<http://www.etree.org/shnutils/mkwcon/>
cust Custom output format module (output only, useful for encoding to a format that shntool does not yet
support)
term sends output to the terminal
null sends output to /dev/null (output only, useful for dry‐runs in several modes, such as fix mode or
strip mode)
shnsplit (part of shntool) definitely supports wavpack if you have wavpack installed (wvunpack is included in wavpack).
I suggest you make sure you have installed cuetools, flac and wavpack. I'm using these tools in Debian and that script decodes and splits cue+wavpack|ape|wav|flac just fine. I think it's reasonable to assume the equivalent packages in Ubuntu are identical except for the version names (this is true of about 70% of Ubuntu packages).
You can check the status of these packages in Synaptic or you can run $ apt-cache policy wavpack
$ apt-cache policy flac
$ apt-cache policy cuetools
This will show you what is installed and what is available in each case.