Let's Encrypt Setup Utility designed for use on a server running VestaCP (https://vestacp.com/) but can be easily modified for use in other environments.

lesu.sh

#!/bin/bash
# Let's Encrypt Setup Utility
# Author: Steven Mirabito <steven@stevenmirabito.com>

letsencrypt_path=/bin/letsencrypt
webroot_template='/home/USER/web/DOMAIN/public_html'
proxy_webroot_template='/home/USER/web/DOMAIN/public_html/static'
cert_path_template='/home/USER/conf/web/ssl.DOMAIN'
account_email='steven@stevtek.com'

function getDomainInfo {
	while true; do
		read -p "Domain name: " input_domain
		if [ -z "$input_domain" ]; then
			echo "Please enter a valid domain name.";
		else
			break;
		fi
	done

	while true; do
		read -p "Username associated with this domain: " input_user
		if [ -z "$input_user" ]; then
			echo "Please enter a valid username.";
		else
			break;
		fi
	done
}

case "${1:-generate}" in
generate)
	getDomainInfo
	
	while true; do
        	read -p "Is this site configured for a proxy pass? [y/n] " input_proxy
                case $input_proxy in
                        [Yy]* ) webroot_tpl=$proxy_webroot_template; break;;
                        [Nn]* ) webroot_tpl=$webroot_template; break;;
                        * ) echo "Please answer yes or no.";;
                esac
	done

	webroot=${webroot_tpl/USER/$input_user}
	webroot=${webroot/DOMAIN/$input_domain}
	
	echo "Requesting certificate..."
	le_result=`${letsencrypt_path} certonly --webroot --webroot-path "${webroot}" --email "${account_email}" --domain "${input_domain}" --agree-tos --renew-by-default`
	echo "$le_result" >> "lesu.log"

	if [[ $le_result == *"Congratulations!"* ]]; then
		echo "Successfully saved certificate files to /etc/letsencrypt/live/${input_domain}"
		echo "See lesu.log for more detailed information."
	else
		echo "Failed to issue certificate. See lesu.log for details."
	fi
	;;
link)
	getDomainInfo
	
	srv_path=${cert_path_template/USER/$input_user}
	srv_path=${srv_path/DOMAIN/$input_domain}
	
	srv_ca="${srv_path}.ca"
	srv_crt="${srv_path}.crt"
	srv_key="${srv_path}.key"
	srv_chain="${srv_path}.pem"
	
	le_ca="/etc/letsencrypt/live/${input_domain}/chain.pem"
	le_crt="/etc/letsencrypt/live/${input_domain}/cert.pem"
	le_key="/etc/letsencrypt/live/${input_domain}/privkey.pem"
	le_chain="/etc/letsencrypt/live/${input_domain}/fullchain.pem"
	
	if [ ! -f "$srv_ca" ] || [ ! -f "$srv_crt" ] || [ ! -f "$srv_key" ] || [ ! -f "$srv_chain" ]; then
		echo "Could not find all required server files. Please ensure you've enabled SSL"
		echo "by copy-and-pasting the certificates into your control panel, then try again."
		exit 1
	fi
	
	if [ ! -f "$le_ca" ] || [ ! -f "$le_crt" ] || [ ! -f "$le_key" ] || [ ! -f "$le_chain" ]; then
		echo "Could not find all required Let's Encrypt files. Please ensure that you've"
		echo "requested a certificate for this domain with Let's Encrypt, then try again."
		exit 1
	fi
	
	echo "Linking certificate files..."
	rm -f $srv_ca $srv_crt $srv_key $srv_chain
	ln -s $le_ca $srv_ca
	ln -s $le_crt $srv_crt
	ln -s $le_key $srv_key
	ln -s $le_chain $srv_chain
	echo "Done!"
	;;
*)
	echo "Usage: $0 [generate|link]"
esac