You may use these Easy Engine commands,
ee site update example.co --letsencrypt=off
ee site update example.co --letsencrypt=on
ee site update example.co --letsencrypt=renew
but only the last one is actually needed to renew the certificate.
If you do not have letsencrypt from some reason you can intall it with
apt-get install letsencrypt
but always good to use the US encoding in your command line.
Note that Let’s Encrypt will not work with cloudflare enabled, since you need to have the original server IP for this.
Make sure also you have the CNAME www.example.co pointing to example.co else the certificate renew or creation will not work.
To automate the process of renew put this into the crontab if this is not already set.
0 0 * * 0 ee site update --le=renew --all 2> /dev/null
This will renew all the sites you have on your system frequently.