Excuse me if this is FAQ thing.
I’ve just cloned github.com/letsencrypt/letsencrypt and tried a ./letsencrypt-auto certonly -a manual -d .
I get an “You will need to bootstrap, configure virtualenv, and run a pip install manually”, looking into that ‘bootstrap’ directory I see a lot of familiar distribution names. In these scripts tools/scripts are called I’ve nerver heard of. I’m running Slackware, what has a rather archaic package system and on the other hand I’m used to compiling Apache/httpd myself and put it where I like it to live.
Getting to the point, what do I need a ‘virtualenv’ and ‘pip’ (whatever that is) for just to generate a certificate.
Again excuse me if I misread the docs and push my nose in the dirt via email, please 
The client is written in python. pip is a package manager for python, while virtualenv is a tool to manage isolated environments for python projects (i.e. foo depends on version x of pip package bar, etc.)
The official client does a lot more than just generating certificates (like automatically configuring web servers, managing a folder structure for certificates, etc); that is the main reasons for all those dependencies.
Take a look at the list of client implementations for various other clients for Let’s Encrypt. Let’s Encrypt uses an open protocol to issue certificates, for which the official client is just one of many implementations, all of which have different goals and use-cases. simp_le and letsencrypt-nosudo are very simple to, have a smaller dependency graph and follow the unix philosophy quite closely, maybe try one of those.