use base 'CGI::Application';
...

sub cgiapp_init {
        ## under FCGI CGI::Application permanently re-inits itself. Not what you would expect from cgiapp_init and setup, anyway...
        ## so we do a hack to get this here executed only once. setup() can be executet over and over
        if(!$self->{remember_app_init_done}){
             # do one time setup stuff here
        }

        ## declare init done
        $self->{remember_app_init_done}=1;
}

sub setup {
        ...

        ## prepare runmodes
        $self->start_mode('default');
        # $self->error_mode('error');
        $self->run_modes();

        ...
}
...