Let’s say we have a big single FLAC file we want to split into multiple files, we are on Fedora and we don’t want to use anything but the command line.
First of all:

[root@fedora ~]$ yum install lame ffmpeg shntool cuetools

To split the single FLAC file run:

[user@fedora ~]$ shnsplit -o flac -f file_name.cue -t "%n - %p - %t" file_name.flac

This will produce n single files, -t parameter is used to specify file name format (in this case: track_number – performer – track_name).
To copy metadata from CUE to the single files run:

[user@fedora ~]$ cuetag.sh file_name.cue *.flac

The following script can be used to convert all the single FLAC files in MP3 (bitrate: 320kb/s) and also copying all the metadata.
Packages needed are lame and id3lib.

#!/bin/bash

for a in *.flac; do
  # give output correct extension
  OUTF="${a[@]/%flac/mp3}"

  # get the tags
  ARTIST=$(metaflac "$a" --show-tag=ARTIST | sed s/.*=//g)
  TITLE=$(metaflac "$a" --show-tag=TITLE | sed s/.*=//g)
  ALBUM=$(metaflac "$a" --show-tag=ALBUM | sed s/.*=//g)
  GENRE=$(metaflac "$a" --show-tag=GENRE | sed s/.*=//g)
  TRACKNUMBER=$(metaflac "$a" --show-tag=TRACKNUMBER | sed s/.*=//g)
  DATE=$(metaflac "$a" --show-tag=DATE | sed s/.*=//g)

  # stream flac into the lame encoder
  flac -c -d "$a" | lame -b 320 --add-id3v2 --pad-id3v2 --ignore-tag-errors \
    --ta "$ARTIST" --tt "$TITLE" --tl "$ALBUM"  --tg "${GENRE:-12}" \
    --tn "${TRACKNUMBER:-0}" --ty "$DATE" - "$OUTF"
done

To convert an ape file in flac run:

[user@fedora ~]$ yum install ffmpeg
[user@fedora ~]$ ffmpeg -i input.ape output.flac