phpmyadmin + LEMP Server on Ubuntu 12.04 (Precise Pangolin)

You can just download phpmyadmin from the site, create a vhost for it in nginx manually and upload the files there. There's no need to do it through apt-get.

I'd recommend doing phpmyadmin via apt-get from a security point of view/ease of management. You just need to do the server configuration yourself which is not hard. I'd even do the apache2 configuration myself… Everyone in the world having the default configuration, and therefore default location for phpmyadmin is a bit of a risk.

In nginx it's simple, something like this is a good starting point (from http://magnatecha.com/set-up-phpmyadmin-with-nginx/):

    server {
        listen          81;
        server_name     localhost;
        root        /usr/share/phpmyadmin;
        index       index.php index.html index.htm;
        if (!-e $request_filename) {
            rewrite ^/(.+)$ /index.php?url=$1 last;
            break;
        }
        location ~ .php$ {
            try_files $uri =404;
            fastcgi_pass unix:/var/run/php5-fpm.sock;
            fastcgi_index index.php;
            include /etc/nginx/fastcgi_params;
        }
    }

Don't just copy and paste that code, I'm assuming you know a little bit about about nginx/php-fpm etc. You'll need to adjust the lines appropriately to your needs and I'd suggest adding additional levels of security (ip address allow/deny at a min).