APE files are, besides lossless audio files, also quite annoying; they're barely supported on non-Windows platforms. There's a way to convert them to FLAC. It took me some time because I had to combine several pieces from the internet in order to convert a single *.ape file to multiple per-track *.flac files.

There are tools for Linux to encode and decode *.ape files. On the internet it is referred as mac-port, but everyone links to a SourceForge page which is dead by now. But I found a tarball from the Slackware servers which does its job. The tarball is also included with this article.