prepare Yubikey with GPG and SSH keys

This article is largely based on ​Eric Severance's blog entry, but updated for gpg2 and my own requirements.

Create .gnupg dir and set correct privileges:

mkdir ~/.gnupg
chmod 700 ~/.gnupg

Avoid an key generation error by:

mkdir -p ~/.gnupg/private-keys-v1.d
chmod 700 ~/.gnupg/private-keys-v1.d

Set GnuPG to prefer strong hash and encryption algorithms

echo "cert-digest-algo SHA512" >> ~/.gnupg/gpg.conf
echo "default-preference-list SHA512 SHA384 SHA256 SHA224 AES256 AES192 AES CAST5 ZLIB BZIP2 ZIP Uncompressed" >> ~/.gnupg/gpg.conf

Install pinentry-tty and modify gpg-agent.conf to get rid of annoying Gnome Shell password prompt.

Create ~/.gnupg/gpg-agent.conf with following content:

pinentry-program /usr/bin/pinentry-tty

Generate key

gpg2 --full-gen-key --expert
gpg (GnuPG) 2.1.15; Copyright (C) 2016 Free Software Foundation, Inc.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

gpg: keybox '/home/jorrit/.gnupg/pubring.kbx' created
Please select what kind of key you want:
   (1) RSA and RSA (default)
   (2) DSA and Elgamal
   (3) DSA (sign only)
   (4) RSA (sign only)
   (7) DSA (set your own capabilities)
   (8) RSA (set your own capabilities)
   (9) ECC and ECC
  (10) ECC (sign only)
  (11) ECC (set your own capabilities)
Your selection? 8

Possible actions for a RSA key: Sign Certify Encrypt Authenticate 
Current allowed actions: Sign Certify Encrypt 

   (S) Toggle the sign capability
   (E) Toggle the encrypt capability
   (A) Toggle the authenticate capability
   (Q) Finished

Your selection? s

Possible actions for a RSA key: Sign Certify Encrypt Authenticate 
Current allowed actions: Certify Encrypt 

   (S) Toggle the sign capability
   (E) Toggle the encrypt capability
   (A) Toggle the authenticate capability
   (Q) Finished

Your selection? e

Possible actions for a RSA key: Sign Certify Encrypt Authenticate 
Current allowed actions: Certify 

   (S) Toggle the sign capability
   (E) Toggle the encrypt capability
   (A) Toggle the authenticate capability
   (Q) Finished

Your selection? q
RSA keys may be between 1024 and 4096 bits long.
What keysize do you want? (2048) 3072
Requested keysize is 3072 bits
Please specify how long the key should be valid.
         0 = key does not expire
      <n>  = key expires in n days
      <n>w = key expires in n weeks
      <n>m = key expires in n months
      <n>y = key expires in n years
Key is valid for? (0) 1y
Key expires at di 24 jul 2018 22:49:09 CEST
Is this correct? (y/N) y

GnuPG needs to construct a user ID to identify your key.

Real name: Jorrit Jorritsma
Email address: jsj@xs4all.nl
Comment: 
You selected this USER-ID:
    "Jorrit Jorritsma <jsj@xs4all.nl>"

Change (N)ame, (C)omment, (E)mail or (O)kay/(Q)uit? o
We need to generate a lot of random bytes. It is a good idea to perform
some other action (type on the keyboard, move the mouse, utilize the
disks) during the prime generation; this gives the random number
generator a better chance to gain enough entropy.
Please enter the passphrase to
protect your new key
Passphrase: 
Repeat: 
gpg: /home/jorrit/.gnupg/trustdb.gpg: trustdb created
gpg: key C2D3C98C511F9CF8 marked as ultimately trusted
gpg: revocation certificate stored as '/home/jorrit/.gnupg/openpgp-revocs.d/94D49EC738E0D9519BCDE7D9C2D3C98C511F9CF8.rev'
public and secret key created and signed.

pub   rsa3072 2017-07-24 [C] [expires: 2018-07-24]
      94D49EC738E0D9519BCDE7D9C2D3C98C511F9CF8
uid                      Jorrit Jorritsma <jsj@xs4all.nl>

Generating the encryption subkey

The next step is to create an encryption subkey. I chose to generate the encryption key using GnuPG, rather than with the Yubikey because private keys that are generated on the Yubikey cannot be removed from the Yubikey. This has a benefit that the private key is never physically on the computer, but it also has the disadvantage that access to all encrypted data is lost if the Yubikey is ever stolen or lost or a new key is generated.

gpg2 --edit-key 94D49EC738E0D9519BCDE7D9C2D3C98C511F9CF8
gpg (GnuPG) 2.1.15; Copyright (C) 2016 Free Software Foundation, Inc.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Secret key is available.

sec  rsa3072/C2D3C98C511F9CF8
     created: 2017-07-24  expires: 2018-07-24  usage: C   
     trust: ultimate      validity: ultimate
[ultimate] (1). Jorrit Jorritsma <jsj@xs4all.nl>

gpg> addkey
Please select what kind of key you want:
   (3) DSA (sign only)
   (4) RSA (sign only)
   (5) Elgamal (encrypt only)
   (6) RSA (encrypt only)
Your selection? 6
RSA keys may be between 1024 and 4096 bits long.
What keysize do you want? (2048) 
Requested keysize is 2048 bits
Please specify how long the key should be valid.
         0 = key does not expire
      <n>  = key expires in n days
      <n>w = key expires in n weeks
      <n>m = key expires in n months
      <n>y = key expires in n years
Key is valid for? (0) 1y
Key expires at di 24 jul 2018 23:15:08 CEST
Is this correct? (y/N) y
Really create? (y/N) y
Please enter the passphrase to unlock the OpenPGP secret key:
"Jorrit Jorritsma <jsj@xs4all.nl>"
3072-bit RSA key, ID C2D3C98C511F9CF8,
created 2017-07-24.

Passphrase: 
We need to generate a lot of random bytes. It is a good idea to perform
some other action (type on the keyboard, move the mouse, utilize the
disks) during the prime generation; this gives the random number
generator a better chance to gain enough entropy.

sec  rsa3072/C2D3C98C511F9CF8
     created: 2017-07-24  expires: 2018-07-24  usage: C   
     trust: ultimate      validity: ultimate
ssb  rsa2048/ED815E1D36A718D2
     created: 2017-07-24  expires: 2018-07-24  usage: E   
[ultimate] (1). Jorrit Jorritsma <jsj@xs4all.nl>

gpg> save

Make a backup of private master keys

mkdir /tmp/gpg
gpg2 -a --export-secret-key 94D49EC738E0D9519BCDE7D9C2D3C98C511F9CF8 > /tmp/gpg/jsj.asc

Make QR codes out of them, as the information is too big to put in one QR code I've decided to generate a QR code per 10 lines and combined in a pdf.

cd /tmp/gpg
split -l 10 jsj.asc
for i in xa*; do cat $i | qrencode -s 10 -t png -o $i.png ; done
convert xa*.png jsj@xs4all.nl.pdf

Print this doc and store it somewhere secure. Recovery can be done with the zbar tools, I zbarcam seems to work best.