Free Let's Encrypt SSL installation can be done from Direct admin panel .You may please follow the below given steps to install the free SSL certificates on your domain .
1. Login to the Direct Admin panel .
2. Select "SSL Certificates" option under "Account Manager".
3. Select the option "Free & automatic certificate from Let's Encrypt " .
4. Select the domains on which you want to install SSL certificates .
5. Click on save .
Once this is done, you can check for the SSL in https://www.sslshopper.com/ssl-checker.html