To use Let’s Encrypt CA to issue free certificates, you need to use their client. The recommended method to install it is to use letsencrypt-auto, a script that automatically fetches and installs all the required dependencies. There is no doubt, that the letsencrypt-auto is the fastest and simplest way to get a Let’s Encrypted client up and running. I’ve used it myself, when I wrote a guide to get Let’s Encrypt up and running easily.
Automatically updating required dependencies, has its downside. As letsencrypt-auto does it every time you run it, it quickly gets annoying. Running a simple ./letsencrypt-auto --help takes a whopping 15 seconds, just figuring out that there are no updates available. Supposing that you know that no update are available, and you wish to save some time, you can run the letsencrypt executable directly, skipping the updating process of lestencrypt-auto:
~/.local/share/letsencrypt/bin/letsencrypt
Most of the actions require you to be root, so you might need to run it with sudo.
You can expect this issue to be resolved in the future. There is already an open issue for it and an active work that will resolve it.
Automatically updating required dependencies, has its downside. As letsencrypt-auto does it every time you run it, it quickly gets annoying.