PhpMyAdmin

Prerequisite

To install PhpMyAdmin, you will need to have Nginx, PHP and MariaDB installed.

Install

# apt install phpmyadmin

The installer will ask you several questions. Here are the answers:

Web server to reconfigure automatically?

Choose none. Nginx will be configured later.

Configure database for phpmyadmin with dbconfig-common?

Yes

Password of the database's administrative user?

Enter your MariaDB root user password.

MySQL application password for phpmyadmin?

Keep it empty to get a random one. You will never need to enter this password

Configure

PHP

Edit file /etc/php5/mods-available/local-common.ini and add folder /usr/share/phpmyadmin/ to the open_basedir setting.

Nginx

Create file /etc/nginx/sites-available/phpmyadmin

server {
    include snippets/listen-http.conf;
    server_name phpmyadmin.example.com;

    access_log /var/log/nginx/phpmyadmin.access.log;
    error_log /var/log/nginx/phpmyadmin.error.log info;

    include snippets/acme-challenge.conf;
    include snippets/https-permanent-redirect.conf;
}

server {
    include snippets/listen-https.conf;
    server_name phpmyadmin.example.com;

    access_log /var/log/nginx/phpmyadmin.access.log;
    error_log /var/log/nginx/phpmyadmin.error.log info;

    include snippets/acme-challenge.conf;

    #include snippets/ssl.conf;
    #ssl_certificate      /etc/letsencrypt/live/phpmyadmin.example.com/fullchain.pem;
    #ssl_certificate_key  /etc/letsencrypt/live/phpmyadmin.example.com/privkey.pem;
    #include snippets/hsts.conf;

    add_header X-Content-Type-Options nosniff;
    add_header X-Frame-Options "SAMEORIGIN";
    add_header X-XSS-Protection "1; mode=block";
    add_header X-Robots-Tag none;

    #auth_basic            "Restricted";
    #auth_basic_user_file  .htpasswd;

    root /usr/share/phpmyadmin/;

    index index.php;

    location ~ \.php$ {
        try_files      $uri =404;
        include fastcgi.conf;
        fastcgi_pass php5;
    }
}

Activate the configuration with

# ln -s /etc/nginx/sites-available/phpmyadmin /etc/nginx/sites-enabled/
# service nginx reload

TLS Certificate

Edit file /usr/local/sbin/renew_certificates and add the following to the config list

{
    'domains': ['phpmyadmin.example.com'],
    'reload': [['service', 'nginx', 'reload']]
}

and get your certificate

# /usr/local/sbin/renew_certificates                           
Renewing certificate for phpmyadmin.example.com that will expire on 0001-01-01



IMPORTANT NOTES:
 - Congratulations! Your certificate and chain have been saved at
   /etc/letsencrypt/live/phpmyadmin.example.com/fullchain.pem. Your
   cert will expire on 2016-10-12. To obtain a new version of the
   certificate in the future, simply run Let's Encrypt again.
 - If you like Let's Encrypt, please consider supporting our work by:

   Donating to ISRG / Let's Encrypt:   https://letsencrypt.org/donate
   Donating to EFF:                    https://eff.org/donate-le

Restarting services:
service nginx reload

Now uncomment the ssl related lines in /etc/nginx/sites-available/phpmyadmin and run

# service nginx reload