I got it to work with the following fixes that I got inspiration from on
the site
https://www.fsfe.org/en/fellows/tyrael/fsfe_card_complete_gnupg_ssh_login_how_to


I added the line 
SUBSYSTEM=="cardman_4040", GROUP="scard", MODE="0660"
to /etc/udev/rules.d/50-pcscd_ccid.rules

Then I added a group called scard and then added myself to that group.
sudo addgroup scard
sudo addgroup YourUserName scard

It didn't work until I rebooted the computer.

-- 
gpg does not recognise Omnikey 4040 Smartcard-reader
https://bugs.launchpad.net/bugs/107337
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