Best way to install skeleton would be Composer, if you didn't install it
Run code in the terminal:
composer create-project ovr/phalcon-module-skeleton=dev-master /path/to/install
First you need to clone the project, update vendors:
git clone https://github.com/ovr/phalcon-module-skeleton.git ./project
cd project
composer update
cp ./docs/configs/nginx.phalcony.local.conf /etc/nginx/sites-enabled/you.host.conf
Don`t forget to edit nginx config and restart nginx:
nano /etc/nginx/sites-enabled/you.host.conf
sudo service nginx restart