I create website example.com on GitHub Pages, and have letsencrypt SSL.
I need SSL on subdomain api.example.com on my VPS.
If I generate a certificate on the server, will the GitHub certificate not be lost?
/etc/certbot-auto certonly --non-interactive --webroot --renew-by-default --agree-tos --expand --email email@example.com --cert-path /etc/letsencrypt/live/example.com/ --chain-path /etc/letsencrypt/live/example.com/ --fullchain-path /etc/letsencrypt/live/example.com/ --key-path /etc/letsencrypt/live/example.com/ --cert-name example.com -w /home/api.example.com/ -d example.com -d www.example.com -d api.example.com
You should only request certificate for sites on your VPS, since you can't serve validation tokens (on your VPS) for the site you had on GitHub.
Only for api.example.com?
/etc/certbot-auto certonly --non-interactive --webroot --renew-by-default --agree-tos --expand --email firstname.lastname@example.org --cert-path /etc/letsencrypt/live/api.example.com/ --chain-path /etc/letsencrypt/live/api.example.com/ --fullchain-path /etc/letsencrypt/live/api.example.com/ --key-path /etc/letsencrypt/live/api.example.com/ --cert-name api.example.com -w /home/api.example.com/ -d api.example.com
If only api.example.com is located in your server.
Yes, api.example.com on server.
example.com on GitHub Pages
Then this command is correct. (Just make sure each argument is correct)
Most of these options are probably not necessary and reflect defaults, or features that probably don't apply to your situation. You would probably also do OK with
/etc/certbot-auto certonly --non-interactive --webroot --agree-tos --email email@example.com -w /home/api.example.com/ -d api.example.com
for a session that must be noninteractive, or even just
/etc/certbot-auto certonly --webroot -w /home/api.example.com/ -d api.example.com
if you're willing to have Certbot interact with you if absolutely necessary. I mostly suggest this because it's easier to read and understand.
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