I have adapted script /etc/X11/Xsession.d/90gpg-agent to:

agent_sock=$(gpgconf --list-dirs agent-socket)
export GPG_AGENT_INFO2=${agent_sock}:0:1
if [ -n "$(gpgconf --list-options gpg-agent | \
      awk -F: '/^enable-ssh-support:/{ print $10 }')" ]; then
    export SSH_AUTH_SOCK=$(gpgconf --list-dirs agent-ssh-socket)
fi

...and after Xsession starts

:~$ echo $GPG_AGENT_INFO2
/run/user/1000/gnupg/S.gpg-agent:0:1

On Wed, 26 Apr 2017 18:33:14 -0700
Daniel Kahn Gillmor <d...@fifthhorseman.net> wrote:

> On Wed 2017-04-26 20:36:25 +0200, Marek Straka wrote:
> >> how does your start X11?  do you have a display manager? if so, which
> >> one?  do you log in from the text-mode console?  
> >
> > I am starting Xfce4 desktop with Lightdm display manager. I tried also
> > to disable Lightdm and start Xsession only with startx command, but
> > variable GPG_AGENT_INFO was also not set.  
> 
> interesting.  What else do you have in /etc/X11/Xsession.d/ ?  are any
> of those scripts being executed?
> 
>    --dkg

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