How can I install application dependencies?

Node.js runs under the nodejs user. To work with Node.js or npm, you must log in as the nodejs user with the command su - nodejs. After switching to the nodejs user you can install packages via npm. Do not forget to go to the directory with the application.

How can I change the application port in the nginx configuration?

Connect to your server via SSH or SFTP. Go to the /etc/nginx/sites-available directory. Open nodejs.conf with any text editor you like. On the proxy_pass http://localhost:3000; line replace port 3000 with the required port. Save the changes and update the Nginx configuration with nginx -s reload command.