If you want to use your yubikey with your own yubico HSM server you need to use this version of mod_authn_yubikey, because the original one does not support do declare your own AuthYkValidationHost and the AuthYkValidationProtocol.
To add the user frank.nord with the password foobar123 and the token id abcdefghijkl you have to do:
htpasswd -csb $your_yubikeyConfigLocation/…/yubikey/ykUserDb abcdefghijkl frank.nord:foobar123
cat ../yubikey/ykUserDb
abcdefghijkl:{SHA}l7xgM5Yq0sDBK6CYZmSwDKuEiAY=
Now you can edit your Apache Config (tested on Apache2 2.2.22-13+deb7u3 with Debian wheezy >=7.5)
<Location /yubitest>
AuthType Basic
AuthBasicProvider yubikey
AuthName "Please Log In using your YubiKey"
AuthYubiKeyTimeout 30
AuthYubiKeyTmpFile yubikey/ykTmpDb
AuthYubiKeyUserFile yubikey/ykUserDb
AuthYubiKeyRequireSecure On
AuthYubiKeyExternalErrorPage Off
AuthYkValidationProtocol https
AuthYkValidationHost api.yubico.com
Require valid-user
</Location>
You can also define your fav. choice of your AuthYkValidationProtocol http or https or …
This has yet to be documented.
Build and upload a current .deb file for simple dpkg -i libapache2-mod-authn-yubikey_$version_amd64.deb because this one inside the Debian apt repository doesn't support this feature.