Let's Encrypt recently enabled support for DNS challenges, but only a few clients yet support it. Lego is one of these clients, and already features integration with a number of popular DNS management APIs, including AWS Route 53, CloudFlare, DigitalOcean, and DNSimple. Lego also makes it really easy to use DNS challenges even without a supported API — if you run it in "manual" DNS challenge mode, it will print out the TXT record you need to add to your zone file, wait for you to add it, and then continue on to complete the challenge.
Lego is a neat Go project that can also itself be used as an API by other Go projects. However, it's quite easy to simply install and run Lego as a command-line tool. These are the steps I took to install it from scratch on Ubuntu 15.10, and use it with Route 53 to generate a SAN SSL certificate (a single certificate covering multiple domain names):
0. Install Go
If you don't already have Go installed on your system, you need to install it first. I don't know exactly what version Lego requires — but something newer than 1.2.1 (the version packaged in Ubuntu 14.04). It does work with version 1.5.1, the version packaged in Ubuntu 15.10, so if you have Ubuntu 15.10 or newer, you can simply install Go via apt-get:
sudo apt-get install golang
Otherwise, the Go Version Manager (GVM) provides a convenient command-line installer, allowing you to install multiple different versions of Go on the same machine, and switch between them as necessary.
1. Install Lego
You can install Lego with the go get command — but if you're not a Go developer, you probably don't have your GOPATH environment variable set, and you need to have it set first. I'd suggest just creating a lego directory somewhere convenient (like in your home folder), and using it for your GOPATH:
mkdir $HOME/lego
export GOPATH=$HOME/lego
go get -u github.com/xenolf/lego
The above will create a lego directory in your home folder, and install the lego executable in its bin subdirectory.
2. Run Lego
Now you can run the lego executable. Specify each domain you want the cert to cover via a separate --domain argument (the example below covers mail.example.com, www.example.com, and example.com). Specify your email address (for renewal reminders) via the --email flag. To use Route 53 DNS validation, include the --dns=route53 flag (for "manual" DNS validation, where you create the challenge DNS records manually, specify --dns=manual instead).
If you use Route 53, first specify your API key and secret as environment variables, like this:
export AWS_ACCESS_KEY_ID=ABC123
export AWS_SECRET_ACCESS_KEY=ABC+def/123
Alternatively, Lego supports the same credential/configuration files that the standard AWS command-line tools support (and uses the Golang Amazon Library specifically, so check out its aws.GetAuth function for the details of exactly what environment variables and configuration files are supported, and in what order they're checked). So if you've got those files set up with your AWS API credentials already, you don't need to mess around with any additional environment variables.
I'd also suggest explicitly specifying the path to the certificates/account info that Lego will generate, via the --path flag; if you created a lego directory in your home folder, just use that:
$HOME/lego/bin/lego \
--accept-tos \
--dns=route53 \
--path=$HOME/lego \
--email=me@example.com \
--domains=mail.example.com \
--domains=www.example.com \
--domains=example.com \
run
3. Check Out the Results
Once run successfully, Lego will output two sets of files into the directory you specified with the --path flag: your Let's Encrypt account info in the accounts subdirectory, and your new SSL cert in the certificates directory:
/home/me/lego/accounts/acme-v01.api.letsencrypt.org/me@example.com/account.json
/home/me/lego/accounts/acme-v01.api.letsencrypt.org/me@example.com/keys/me@example.com.key
/home/me/lego/certificates/mail.example.com.crt
/home/me/lego/certificates/mail.example.com.json
/home/me/lego/certificates/mail.example.com.key
In the accounts hierarchy, the account.json file contains your Let's Encrypt account info (which you can use later to renew or revoke the certificate). The me@example.com.key contains the secret key (ie password) for that account.
In the certificates subdirectory, your new certificate file will be named with the first domain you specified (in the above example, mail.example.com), with a crt extension. This file also includes the intermediate certificate for Let's Encrypt, so it's equivalent to the "fullchain" file that the reference Let's Encrypt client generates (the so-called "all-in-one" file that you'd use with Apache's SSLCertificateFile directive or Nginx's ssl_certificate directive). The corresponding secret key for the certificate will have the same name, but with a key extension. The file with the json extension contains some (non-secret) metadata for the cert that Let's Encrypt will need later if you renew or revoke it.
If you have OpenSSL installed, you can check out the cert details with this command (which will print out the details to stdout):
openssl x509 -text -noout -in $HOME/lego/certificates/mail.example.com.crt
The different domain names the cert covers will be listed in the X509v3 Subject Alternative Name field of the output.