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Guide to using YubiKey for GPG and SSH

gnupg gpg gpg-agent gpg-configuration remote-access rsa-cryptography security smartcard ssh yubikey

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Dawid Łakomski 07752240cb Add information about composite USB mode on YK with firmware >=3.3		2017-05-12 09:04:23 +02:00
LICENSE	Initial commit	2016-01-31 20:56:50 -05:00
README.md	Add information about composite USB mode on YK with firmware >=3.3	2017-05-12 09:04:23 +02:00

README.md

This is a practical guide to using YubiKey as a SmartCard for storing GPG encryption and signing keys.

An authentication key can also be created for SSH and used with gpg-agent.

Keys stored on a smartcard like YubiKey seem more difficult to steal than ones stored on disk, and are convenient for everyday use.

Instructions written for Debian GNU/Linux 8 (jessie) using YubiKey 4 in OTP+CCID mode. Note, older YubiKeys are limited to 2048 bit RSA keys.

Debian live install images are available from here and are suitable for writing to USB drives.

Programming YubiKey for GPG keys still lets you use its two slots - OTP and static password modes, for example.

If you have a comment or suggestion, please open an issue on GitHub.

Purchase YubiKey
Install required software
Creating keys
Using keys
Troubleshooting
References

Purchase YubiKey

https://www.yubico.com/products/yubikey-hardware/

https://www.yubico.com/store/

https://www.amazon.com/Yubico/b/ref=bl_dp_s_web_10358012011?ie=UTF8&node=10358012011

Consider purchasing a pair and programming both in case of loss or damage to one of them.

Install required software

You will need to install the following software:

$ sudo apt-get install -y gnupg2 gnupg-agent pinentry-curses scdaemon pcscd yubikey-personalization libusb-1.0-0-dev

You may also need to download and install more recent versions of yubikey-personalization and yubico-c:

$ curl -sO https://developers.yubico.com/yubikey-personalization/Releases/ykpers-1.17.3.tar.gz

$ !!.sig
curl -sO https://developers.yubico.com/yubikey-personalization/Releases/ykpers-1.17.3.tar.gz.sig

$ gpg ykpers*sig
gpg: assuming signed data in `ykpers-1.17.3.tar.gz'
gpg: Signature made Mon 28 Dec 2015 11:56:41 AM UTC
gpg:                using RSA key 0xBCA00FD4B2168C0A
gpg: Can't check signature: public key not found

$ gpg --recv 0xBCA00FD4B2168C0A
gpg: requesting key 0xBCA00FD4B2168C0A from hkps server hkps.pool.sks-keyservers.net
mp/2.3
[...]
gpg: key 0xBCA00FD4B2168C0A: public key "Klas Lindfors <klas@yubico.com>" imported
gpg: 3 marginal(s) needed, 1 complete(s) needed, PGP trust model
gpg: depth: 0  valid:   1  signed:   0  trust: 0-, 0q, 0n, 0m, 0f, 1u
gpg: Total number processed: 1
gpg:               imported: 1  (RSA: 1)

$ gpg ykpers*sig
gpg: assuming signed data in `ykpers-1.17.3.tar.gz'
gpg: Signature made Mon 28 Dec 2015 11:56:41 AM UTC
gpg:                using RSA key 0xBCA00FD4B2168C0A
gpg: Good signature from "Klas Lindfors <klas@yubico.com>" [unknown]
gpg: WARNING: This key is not certified with a trusted signature!
gpg:          There is no indication that the signature belongs to the owner.
Primary key fingerprint: 0A3B 0262 BCA1 7053 07D5  FF06 BCA0 0FD4 B216 8C0A

$ curl -sO https://developers.yubico.com/yubico-c/Releases/libyubikey-1.13.tar.gz

$ !!.sig
curl -sO https://developers.yubico.com/yubico-c/Releases/libyubikey-1.13.tar.gz.sig

$ gpg libyubi*sig
gpg: assuming signed data in `libyubikey-1.13.tar.gz'
gpg: Signature made Thu 05 Mar 2015 11:51:51 AM UTC
gpg:                using RSA key 0xBCA00FD4B2168C0A
gpg: Good signature from "Klas Lindfors <klas@yubico.com>" [unknown]
gpg: WARNING: This key is not certified with a trusted signature!
gpg:          There is no indication that the signature belongs to the owner.
Primary key fingerprint: 0A3B 0262 BCA1 7053 07D5  FF06 BCA0 0FD4 B216 8C0A

$ tar xf libyubikey-1.13.tar.gz

$ cd libyubikey-1.13

$ ./configure && make && sudo make install

$ cd ..

$ tar xf ykpers-1.17.3.tar.gz

$ cd ykpers-1.17.3

$ ./configure && make && sudo make install

$ sudo ldconfig

If on Tails, you also need to install libykpers-1-1 from the testing repository. This is a temporary fix suggested on a securedrop issue:

$ sudo apt-get install -t testing libykpers-1-1

Creating keys

Create temporary working directory for GPG

Create a directory in /tmp which won't survive a reboot:

$ export GNUPGHOME=$(mktemp -d) ; echo $GNUPGHOME
/tmp/tmp.aaiTTovYgo

Create configuration

Paste the following text into a terminal window to create a recommended GPG configuration:

$ cat << EOF > $GNUPGHOME/gpg.conf
use-agent
personal-cipher-preferences AES256 AES192 AES CAST5
personal-digest-preferences SHA512 SHA384 SHA256 SHA224
default-preference-list SHA512 SHA384 SHA256 SHA224 AES256 AES192 AES CAST5 ZLIB BZIP2 ZIP Uncompressed
cert-digest-algo SHA512
s2k-digest-algo SHA512
s2k-cipher-algo AES256
charset utf-8
fixed-list-mode
no-comments
no-emit-version
keyid-format 0xlong
list-options show-uid-validity
verify-options show-uid-validity
with-fingerprint
EOF

Create master key

Generate a new key with GPG, selecting RSA (sign only) and the appropriate keysize, optionally specifying an expiry:

$ gpg --gen-key

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)
Your selection? 4
RSA keys may be between 1024 and 4096 bits long.
What keysize do you want? (2048) 4096
Requested keysize is 4096 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) 0
Key does not expire at all
Is this correct? (y/N) y

You need a user ID to identify your key; the software constructs the user ID
from the Real Name, Comment and Email Address in this form:
    "Heinrich Heine (Der Dichter) <heinrichh@duesseldorf.de>"

Real name: Dr Duh
Email address: doc@duh.to
Comment:
You selected this USER-ID:
    "Dr Duh <doc@duh.to>"

Change (N)ame, (C)omment, (E)mail or (O)kay/(Q)uit? o
You need a Passphrase to protect your secret key.

gpg: key 0xFF3E7D88647EBCDB marked as ultimately trusted
public and secret key created and signed.

gpg: checking the trustdb
gpg: 3 marginal(s) needed, 1 complete(s) needed, PGP trust model
gpg: depth: 0  valid:   1  signed:   0  trust: 0-, 0q, 0n, 0m, 0f, 1u
pub   4096R/0xFF3E7D88647EBCDB 2016-05-24
      Key fingerprint = 011C E16B D45B 27A5 5BA8  776D FF3E 7D88 647E BCDB
uid                 [ultimate] Dr Duh <doc@duh.to>

Note that this key cannot be used for encryption.  You may want to use
the command "--edit-key" to generate a subkey for this purpose.

Keep this passphrase handy as you'll need it throughout.

Save Key ID

Export the key ID as a variable for use throughout:

$ KEYID=0xFF3E7D88647EBCDB

Create revocation certificate

Create a way to revoke your keys in case of loss or compromise, an explicit reason being optional:

$ gpg --gen-revoke $KEYID > $GNUPGHOME/revoke.txt

sec  4096R/0xFF3E7D88647EBCDB 2016-05-24 Dr Duh <doc@duh.to>

Create a revocation certificate for this key? (y/N) y
Please select the reason for the revocation:
  0 = No reason specified
  1 = Key has been compromised
  2 = Key is superseded
  3 = Key is no longer used
  Q = Cancel
(Probably you want to select 1 here)
Your decision? 1
Enter an optional description; end it with an empty line:
>
Reason for revocation: Key has been compromised
(No description given)
Is this okay? (y/N) y

You need a passphrase to unlock the secret key for
user: "Dr Duh <doc@duh.to>"
4096-bit RSA key, ID 0xFF3E7D88647EBCDB, created 2016-05-24

ASCII armored output forced.
Revocation certificate created.

Please move it to a medium which you can hide away; if Mallory gets
access to this certificate he can use it to make your key unusable.
It is smart to print this certificate and store it away, just in case
your media become unreadable.  But have some caution:  The print system of
your machine might store the data and make it available to others!

Back up master key

Save a copy of the private key block:

$ gpg --armor --export-secret-keys $KEYID > $GNUPGHOME/master.key

Create subkeys

Edit the key to add subkeys:

$ gpg --expert --edit-key $KEYID

Secret key is available.

pub  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never       usage: SC
                               trust: ultimate      validity: ultimate
[ultimate] (1). Dr Duh <doc@duh.to>

Signing key

First, create a signing key, selecting RSA (sign only):

gpg> addkey
Key is protected.

You need a passphrase to unlock the secret key for
user: "Dr Duh <doc@duh.to>"
4096-bit RSA key, ID 0xFF3E7D88647EBCDB, created 2016-05-24

Please select what kind of key you want:
   (3) DSA (sign only)
   (4) RSA (sign only)
   (5) Elgamal (encrypt only)
   (6) RSA (encrypt only)
   (7) DSA (set your own capabilities)
   (8) RSA (set your own capabilities)
Your selection? 4
RSA keys may be between 1024 and 4096 bits long.
What keysize do you want? (2048) 4096
Requested keysize is 4096 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) 0
Key does not expire at all
Is this correct? (y/N) y
Really create? (y/N) y
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.

...................+++++
..+++++

pub  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never       usage: SC
                               trust: ultimate      validity: ultimate
sub  4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never       usage: S
[ultimate] (1). Dr Duh <doc@duh.to>

Encryption key

Next, create an encryption key, selecting RSA (encrypt only):

gpg> addkey
Key is protected.

You need a passphrase to unlock the secret key for
user: "Dr Duh <doc@duh.to>"
4096-bit RSA key, ID 0xFF3E7D88647EBCDB, created 2016-05-24

Please select what kind of key you want:
   (3) DSA (sign only)
   (4) RSA (sign only)
   (5) Elgamal (encrypt only)
   (6) RSA (encrypt only)
   (7) DSA (set your own capabilities)
   (8) RSA (set your own capabilities)
Your selection? 6
RSA keys may be between 1024 and 4096 bits long.
What keysize do you want? (2048) 4096
Requested keysize is 4096 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) 0
Key does not expire at all
Is this correct? (y/N) y
Really create? (y/N) y
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.

.+++++
...........+++++

pub  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never       usage: SC
                               trust: ultimate      validity: ultimate
sub  4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never       usage: S
sub  4096R/0x5912A795E90DD2CF  created: 2016-05-24  expires: never       usage: E
[ultimate] (1). Dr Duh <doc@duh.to>

Authentication key

Finally, create an authentication key, selecting RSA (set your own capabilities):

gpg> addkey
Key is protected.

You need a passphrase to unlock the secret key for
user: "Dr Duh <doc@duh.to>"
4096-bit RSA key, ID 0xFF3E7D88647EBCDB, created 2016-05-24

Please select what kind of key you want:
   (3) DSA (sign only)
   (4) RSA (sign only)
   (5) Elgamal (encrypt only)
   (6) RSA (encrypt only)
   (7) DSA (set your own capabilities)
   (8) RSA (set your own capabilities)
Your selection? 8

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

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

Your selection? a

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

   (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) 4096
Requested keysize is 4096 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) 0
Key does not expire at all
Is this correct? (y/N) y
Really create? (y/N) y
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.

+++++
.....+++++

pub  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never       usage: SC
                               trust: ultimate      validity: ultimate
sub  4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never       usage: S
sub  4096R/0x5912A795E90DD2CF  created: 2016-05-24  expires: never       usage: E
sub  4096R/0x3F29127E79649A3D  created: 2016-05-24  expires: never       usage: A
[ultimate] (1). Dr Duh <doc@duh.to>

gpg> save

Check your work

List your new secret keys:

$ gpg --list-secret-keys
/tmp/tmp.aaiTTovYgo/secring.gpg
-------------------------------
sec   4096R/0xFF3E7D88647EBCDB 2016-05-24
      Key fingerprint = 011C E16B D45B 27A5 5BA8  776D FF3E 7D88 647E BCDB
uid                            Dr Duh <doc@duh.to>
ssb   4096R/0xBECFA3C1AE191D15 2016-05-24
ssb   4096R/0x5912A795E90DD2CF 2016-05-24
ssb   4096R/0x3F29127E79649A3D 2016-05-24

Verify with OpenPGP key checks:

Use the automated key best practice checker:

$ sudo apt-get install hopenpgp-tools
$ hkt export-pubkeys $KEYID | hokey lint

The output will display any problems with your key in red text. If everything is green, your key passes each of the tests below. If it is red, your key has failed one of the tests.

Export subkeys

Save a copy of your subkeys:

$ gpg --armor --export-secret-keys $KEYID > $GNUPGHOME/mastersub.key

$ gpg --armor --export-secret-subkeys $KEYID > $GNUPGHOME/sub.key

Back up everything

Once keys are moved to hardware, they cannot be extracted again (otherwise, what would be the point?), so make sure you have made an encrypted backup before proceeding.

To create an encrypted USB drive, first attach it and check its label:

$ dmesg | tail
[ 7667.607011] scsi8 : usb-storage 2-1:1.0
[ 7667.608766] usbcore: registered new interface driver usb-storage
[ 7668.874016] scsi 8:0:0:0: USB 0: 0 ANSI: 6
[ 7668.874242] sd 8:0:0:0: Attached scsi generic sg4 type 0
[ 7668.874682] sd 8:0:0:0: [sde] 62980096 512-byte logical blocks: (32.2 GB/30.0 GiB)
[ 7668.875022] sd 8:0:0:0: [sde] Write Protect is off
[ 7668.875023] sd 8:0:0:0: [sde] Mode Sense: 43 00 00 00
[ 7668.877939]  sde: sde1
[ 7668.879514] sd 8:0:0:0: [sde] Attached SCSI removable disk

Check the size to make sure it's the right drive:

$ sudo fdisk -l | grep /dev/sde
Disk /dev/sde: 30 GiB, 32245809152 bytes, 62980096 sectors
/dev/sde1        2048 62980095 62978048  30G  6 FAT16

Erase and create a new partition table:

$ sudo fdisk /dev/sde

Welcome to fdisk (util-linux 2.25.2).
Changes will remain in memory only, until you decide to write them.
Be careful before using the write command.

Command (m for help): o
Created a new DOS disklabel with disk identifier 0xeac7ee35.

Command (m for help): w
The partition table has been altered.
Calling ioctl() to re-read partition table.
Syncing disks.

Remove and reinsert the USB drive, then create a new partition, selecting defaults::

$ sudo fdisk /dev/sde

Welcome to fdisk (util-linux 2.25.2).
Changes will remain in memory only, until you decide to write them.
Be careful before using the write command.

Command (m for help): n
Partition type
   p   primary (0 primary, 0 extended, 4 free)
   e   extended (container for logical partitions)
Select (default p): p
Partition number (1-4, default 1): 1
First sector (2048-62980095, default 2048):
Last sector, +sectors or +size{K,M,G,T,P} (2048-62980095, default 62980095):

Created a new partition 1 of type 'Linux' and of size 30 GiB.
Command (m for help): w
The partition table has been altered.
Calling ioctl() to re-read partition table.
Syncing disks.

Use LUKS to encrypt the new partition:

$ sudo cryptsetup luksFormat /dev/sde1

WARNING!
========
This will overwrite data on /dev/sde1 irrevocably.

Are you sure? (Type uppercase yes): YES
Enter passphrase:
Verify passphrase:

Mount the partition:

$ sudo cryptsetup luksOpen /dev/sde1 encrypted-usb
Enter passphrase for /dev/sde1:

Create a filesystem:

$ sudo mkfs.ext4 /dev/mapper/encrypted-usb -L encrypted-usb
mke2fs 1.42.12 (29-Aug-2014)
Creating filesystem with 7871744 4k blocks and 1970416 inodes
Superblock backups stored on blocks:
        32768, 98304, 163840, 229376, 294912, 819200, 884736, 1605632, 2654208,
        4096000

Allocating group tables: done
Writing inode tables: done
Creating journal (32768 blocks): done
Writing superblocks and filesystem accounting information: done

Mount the filesystem:

$ sudo mkdir /mnt/usb
$ sudo mount /dev/mapper/encrypted-usb /mnt/usb

Finally, copy files to it:

$ sudo cp -avi $GNUPGHOME /mnt/usb
‘/tmp/tmp.aaiTTovYgo’ -> ‘/mnt/usb/tmp.aaiTTovYgo’
‘/tmp/tmp.aaiTTovYgo/revoke.txt’ -> ‘/mnt/usb/tmp.aaiTTovYgo/revoke.txt’
‘/tmp/tmp.aaiTTovYgo/gpg.conf’ -> ‘/mnt/usb/tmp.aaiTTovYgo/gpg.conf’
‘/tmp/tmp.aaiTTovYgo/trustdb.gpg’ -> ‘/mnt/usb/tmp.aaiTTovYgo/trustdb.gpg’
‘/tmp/tmp.aaiTTovYgo/random_seed’ -> ‘/mnt/usb/tmp.aaiTTovYgo/random_seed’
‘/tmp/tmp.aaiTTovYgo/master.key’ -> ‘/mnt/usb/tmp.aaiTTovYgo/master.key’
‘/tmp/tmp.aaiTTovYgo/secring.gpg’ -> ‘/mnt/usb/tmp.aaiTTovYgo/secring.gpg’
‘/tmp/tmp.aaiTTovYgo/mastersub.key’ -> ‘/mnt/usb/tmp.aaiTTovYgo/mastersub.key’
‘/tmp/tmp.aaiTTovYgo/sub.key’ -> ‘/mnt/usb/tmp.aaiTTovYgo/sub.key’
‘/tmp/tmp.aaiTTovYgo/pubring.gpg~’ -> ‘/mnt/usb/tmp.aaiTTovYgo/pubring.gpg~’
‘/tmp/tmp.aaiTTovYgo/pubring.gpg’ -> ‘/mnt/usb/tmp.aaiTTovYgo/pubring.gpg’

Make sure the correct files were copied, then unmount and disconnected the encrypted USB drive:

$ sudo umount /mnt/usb
$ sudo cryptsetup luksClose encrypted-usb

Configure YubiKey

Plug in your YubiKey and configure it:

$ ykpersonalize -m82
Firmware version 4.2.7 Touch level 527 Program sequence 4

The USB mode will be set to: 0x82

Commit? (y/n) [n]: y

The -m option is the mode command. To see the different modes, enter ykpersonalize –help. Mode 82 (in hex) enables the YubiKey NEO as a composite USB device (HID + CCID) and allows OTPs to be emitted while in use as a smart card. Once you have changed the mode, you need to re-boot the YubiKey – so remove and re-insert it.

On YubiKey NEO with firmware version 3.3 or higher you can enable composite USB device with -m86 instead of -m82.

https://www.yubico.com/2012/12/yubikey-neo-openpgp/ https://www.yubico.com/2012/12/yubikey-neo-composite-device/

Configure smartcard

Use GPG to configure YubiKey as a smartcard:

$ gpg --card-edit

Application ID ...: D2760001240102010006055532110000
Version ..........: 2.1
Manufacturer .....: unknown
Serial number ....: 05553211
Name of cardholder: [not set]
Language prefs ...: [not set]
Sex ..............: unspecified
URL of public key : [not set]
Login data .......: [not set]
Private DO 1 .....: [not set]
Private DO 2 .....: [not set]
Signature PIN ....: not forced
Key attributes ...: 2048R 2048R 2048R
Max. PIN lengths .: 127 127 127
PIN retry counter : 3 3 3
Signature counter : 0
Signature key ....: [none]
Encryption key....: [none]
Authentication key: [none]
General key info..: [none]

Change PINs

The default PIN codes are 12345678 and 123456.

gpg/card> admin
Admin commands are allowed

gpg/card> passwd
gpg: OpenPGP card no. D2760001240102010006055532110000 detected

1 - change PIN
2 - unblock PIN
3 - change Admin PIN
4 - set the Reset Code
Q - quit

Your selection? 3
PIN changed.

1 - change PIN
2 - unblock PIN
3 - change Admin PIN
4 - set the Reset Code
Q - quit

1 - change PIN
2 - unblock PIN
3 - change Admin PIN
4 - set the Reset Code
Q - quit

Your selection? 1
PIN changed.

1 - change PIN
2 - unblock PIN
3 - change Admin PIN
4 - set the Reset Code
Q - quit

Your selection? q

Set card information

Some fields are optional:

gpg/card> name
Cardholder's surname: Duh
Cardholder's given name: Dr

gpg/card> lang
Language preferences: en

gpg/card> login
Login data (account name): doc@duh.to

gpg/card> (Press Enter)

Application ID ...: D2760001240102010006055532110000
Version ..........: 2.1
Manufacturer .....: unknown
Serial number ....: 05553211
Name of cardholder: Dr Duh
Language prefs ...: en
Sex ..............: unspecified
URL of public key : [not set]
Login data .......: doc@duh.to
Private DO 4 .....: [not set]
Signature PIN ....: not forced
Key attributes ...: 2048R 2048R 2048R
Max. PIN lengths .: 127 127 127
PIN retry counter : 3 3 3
Signature counter : 0
Signature key ....: [none]
Encryption key....: [none]
Authentication key: [none]
General key info..: [none]

gpg/card> quit

Transfer keys

Transfering keys to YubiKey hardware is a one-way operation only, so make sure you've made a backup before proceeding:

$ gpg --edit-key $KEYID

Secret key is available.

pub  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never       usage: SC
                               trust: ultimate      validity: ultimate
sub  4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never       usage: S
sub  4096R/0x5912A795E90DD2CF  created: 2016-05-24  expires: never       usage: E
sub  4096R/0x3F29127E79649A3D  created: 2016-05-24  expires: never       usage: A
[ultimate] (1). Dr Duh <doc@duh.to>

gpg> toggle

sec  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never
ssb  4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never
ssb  4096R/0x5912A795E90DD2CF  created: 2016-05-24  expires: never
ssb  4096R/0x3F29127E79649A3D  created: 2016-05-24  expires: never
(1)  Dr Duh <doc@duh.to>

gpg> key 1

sec  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never
ssb* 4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never
ssb  4096R/0x5912A795E90DD2CF  created: 2016-05-24  expires: never
ssb  4096R/0x3F29127E79649A3D  created: 2016-05-24  expires: never
(1)  Dr Duh <doc@duh.to>

Signature key

Move the signature key (you will be prompted for the key passphrase and admin PIN):

gpg> keytocard
Signature key ....: [none]
Encryption key....: [none]
Authentication key: [none]

Please select where to store the key:
   (1) Signature key
   (3) Authentication key
Your selection? 1

You need a passphrase to unlock the secret key for
user: "Dr Duh <doc@duh.to>"
4096-bit RSA key, ID 0xBECFA3C1AE191D15, created 2016-05-24


sec  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never
ssb* 4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never
                     card-no: 0006 05553211
ssb  4096R/0x5912A795E90DD2CF  created: 2016-05-24  expires: never
ssb  4096R/0x3F29127E79649A3D  created: 2016-05-24  expires: never
(1)  Dr Duh <doc@duh.to>

Encryption key

Type key 1 again to deselect and key 2 to select the next key:

gpg> key 1

sec  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never
ssb  4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never
                     card-no: 0006 05553211
ssb  4096R/0x5912A795E90DD2CF  created: 2016-05-24  expires: never
ssb  4096R/0x3F29127E79649A3D  created: 2016-05-24  expires: never
(1)  Dr Duh <doc@duh.to>

gpg> key 2

sec  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never
ssb  4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never
                     card-no: 0006 05553211
ssb* 4096R/0x5912A795E90DD2CF  created: 2016-05-24  expires: never
ssb  4096R/0x3F29127E79649A3D  created: 2016-05-24  expires: never
(1)  Dr Duh <doc@duh.to>

Move the encryption key to card:

gpg> keytocard
Signature key ....: 07AA 7735 E502 C5EB E09E  B8B0 BECF A3C1 AE19 1D15
Encryption key....: [none]
Authentication key: [none]

Please select where to store the key:
   (2) Encryption key
Your selection? 2

You need a passphrase to unlock the secret key for
user: "Dr Duh <doc@duh.to>"
4096-bit RSA key, ID 0x5912A795E90DD2CF, created 2016-05-24

sec  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never
ssb  4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never
                     card-no: 0006 05553211
ssb* 4096R/0x5912A795E90DD2CF  created: 2016-05-24  expires: never
                     card-no: 0006 05553211
ssb  4096R/0x3F29127E79649A3D  created: 2016-05-24  expires: never
(1)  Dr Duh <doc@duh.to>

Authentication key

Type key 2 again to deselect and key 3 to select the next key:

gpg> key 2

sec  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never
ssb  4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never
                     card-no: 0006 05553211
ssb  4096R/0x5912A795E90DD2CF  created: 2016-05-24  expires: never
                     card-no: 0006 05553211
ssb  4096R/0x3F29127E79649A3D  created: 2016-05-24  expires: never
(1)  Dr Duh <doc@duh.to>

gpg> key 3

sec  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never
ssb  4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never
                     card-no: 0006 05553211
ssb  4096R/0x5912A795E90DD2CF  created: 2016-05-24  expires: never
                     card-no: 0006 05553211
ssb* 4096R/0x3F29127E79649A3D  created: 2016-05-24  expires: never
(1)  Dr Duh <doc@duh.to>

Move the authentication key to card:

gpg> keytocard
Signature key ....: 07AA 7735 E502 C5EB E09E  B8B0 BECF A3C1 AE19 1D15
Encryption key....: 6F26 6F46 845B BEB8 BDF3  7E9B 5912 A795 E90D D2CF
Authentication key: [none]

Please select where to store the key:
   (3) Authentication key
Your selection? 3

You need a passphrase to unlock the secret key for
user: "Dr Duh <doc@duh.to>"
4096-bit RSA key, ID 0x3F29127E79649A3D, created 2016-05-24

sec  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never
ssb  4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never
                     card-no: 0006 05553211
ssb  4096R/0x5912A795E90DD2CF  created: 2016-05-24  expires: never
                     card-no: 0006 05553211
ssb* 4096R/0x3F29127E79649A3D  created: 2016-05-24  expires: never
                     card-no: 0006 05553211
(1)  Dr Duh <doc@duh.to>

Save and quit:

gpg> save

Check your work

ssb> indicates a stub to the private key on smartcard:

$ gpg --list-secret-keys
/tmp/tmp.aaiTTovYgo/secring.gpg
-------------------------------
sec   4096R/0xFF3E7D88647EBCDB 2016-05-24
      Key fingerprint = 011C E16B D45B 27A5 5BA8  776D FF3E 7D88 647E BCDB
uid                            Dr Duh <doc@duh.to>
ssb>  4096R/0xBECFA3C1AE191D15 2016-05-24
ssb>  4096R/0x5912A795E90DD2CF 2016-05-24
ssb>  4096R/0x3F29127E79649A3D 2016-05-24

Export public key

This file should be publicly shared:

$ gpg --armor --export $KEYID > /mnt/public-usb-key/pubkey.txt

Optionally, it may be uploaded to a public keyserver:

$ gpg --send-key $KEYID
gpg: sending key 0xFF3E7D88647EBCDB to hkps server hkps.pool.sks-keyservers.net
[...]

After a little while, it ought to propagate to other servers.

Finish

If all went well, you should now reboot or securely delete $GNUPGHOME.

Using keys

Create GPG configuration

Paste the following text into a terminal window to create a recommended GPG configuration:

$ cat << EOF > ~/.gnupg/gpg.conf
auto-key-locate keyserver
keyserver hkps://hkps.pool.sks-keyservers.net
keyserver-options no-honor-keyserver-url
keyserver-options ca-cert-file=/etc/sks-keyservers.netCA.pem
keyserver-options no-honor-keyserver-url
keyserver-options debug
keyserver-options verbose
personal-cipher-preferences AES256 AES192 AES CAST5
personal-digest-preferences SHA512 SHA384 SHA256 SHA224
default-preference-list SHA512 SHA384 SHA256 SHA224 AES256 AES192 AES CAST5 ZLIB BZIP2 ZIP Uncompressed
cert-digest-algo SHA512
s2k-cipher-algo AES256
s2k-digest-algo SHA512
charset utf-8
fixed-list-mode
no-comments
no-emit-version
keyid-format 0xlong
list-options show-uid-validity
verify-options show-uid-validity
with-fingerprint
use-agent
require-cross-certification
EOF

To install the keyservers CA file:

$ sudo curl -s "https://sks-keyservers.net/sks-keyservers.netCA.pem" -o /etc/sks-keyservers.netCA.pem

Import public key

Import it from a file:

$ gpg --import < /mnt/public-usb-key/pubkey.txt
gpg: key 0xFF3E7D88647EBCDB: public key "Dr Duh <doc@duh.to>" imported
gpg: Total number processed: 1
gpg:               imported: 1  (RSA: 1)

Or download from a keyserver:

$ gpg --recv 0xFF3E7D88647EBCDB
gpg: requesting key 0xFF3E7D88647EBCDB from hkps server hkps.pool.sks-keyservers.net
[...]
gpg: key 0xFF3E7D88647EBCDB: public key "Dr Duh <doc@duh.to>" imported
gpg: Total number processed: 1
gpg:               imported: 1  (RSA: 1)

You may get an error gpgkeys: HTTP fetch error 1: unsupported protocol -- this means you need to install a special version of curl which supports gnupg:

$ sudo apt-get install gnupg-curl

Insert YubiKey

Check the card's status:

$ gpg --card-status
Application ID ...: D2760001240102010006055532110000
Version ..........: 2.1
Manufacturer .....: Yubico
Serial number ....: 05553211
Name of cardholder: Dr Duh
Language prefs ...: en
Sex ..............: unspecified
URL of public key : [not set]
Login data .......: doc@duh.to
Signature PIN ....: not forced
Key attributes ...: 4096R 4096R 4096R
Max. PIN lengths .: 127 127 127
PIN retry counter : 3 3 3
Signature counter : 0
Signature key ....: 07AA 7735 E502 C5EB E09E  B8B0 BECF A3C1 AE19 1D15
      created ....: 2016-05-24 23:22:01
Encryption key....: 6F26 6F46 845B BEB8 BDF3  7E9B 5912 A795 E90D D2CF
      created ....: 2016-05-24 23:29:03
Authentication key: 82BE 7837 6A3F 2E7B E556  5E35 3F29 127E 7964 9A3D
      created ....: 2016-05-24 23:36:40
General key info..: pub  4096R/0xBECFA3C1AE191D15 2016-05-24 Dr Duh <doc@duh.to>
sec#  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never
ssb>  4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never
                      card-no: 0006 05553211
ssb>  4096R/0x5912A795E90DD2CF  created: 2016-05-24  expires: never
                      card-no: 0006 05553211
ssb>  4096R/0x3F29127E79649A3D  created: 2016-05-24  expires: never
                      card-no: 0006 05553211

sec# indicates master key is not available (as it should be stored encrypted offline).

GnuPG

Trust master key

Edit the imported key to assign it ultimate trust:

$ gpg --edit-key 0xFF3E7D88647EBCDB

Secret key is available.

pub  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never       usage: SC
                               trust: unknown       validity: unknown
sub  4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never       usage: S
sub  4096R/0x5912A795E90DD2CF  created: 2016-05-24  expires: never       usage: E
sub  4096R/0x3F29127E79649A3D  created: 2016-05-24  expires: never       usage: A
[ unknown] (1). Dr Duh <doc@duh.to>

gpg> trust
pub  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never       usage: SC
                               trust: unknown       validity: unknown
sub  4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never       usage: S
sub  4096R/0x5912A795E90DD2CF  created: 2016-05-24  expires: never       usage: E
sub  4096R/0x3F29127E79649A3D  created: 2016-05-24  expires: never       usage: A
[ unknown] (1). Dr Duh <doc@duh.to>

Please decide how far you trust this user to correctly verify other users' keys
(by looking at passports, checking fingerprints from different sources, etc.)

  1 = I don't know or won't say
  2 = I do NOT trust
  3 = I trust marginally
  4 = I trust fully
  5 = I trust ultimately
  m = back to the main menu

Your decision? 5
Do you really want to set this key to ultimate trust? (y/N) y

pub  4096R/0xFF3E7D88647EBCDB  created: 2016-05-24  expires: never       usage: SC
                               trust: ultimate      validity: unknown
sub  4096R/0xBECFA3C1AE191D15  created: 2016-05-24  expires: never       usage: S
sub  4096R/0x5912A795E90DD2CF  created: 2016-05-24  expires: never       usage: E
sub  4096R/0x3F29127E79649A3D  created: 2016-05-24  expires: never       usage: A
[ unknown] (1). Dr Duh <doc@duh.to>
Please note that the shown key validity is not necessarily correct
unless you restart the program.

gpg> quit

Encryption

Encrypt some sample text:

$ echo "$(uname -a)" | gpg --encrypt --armor --recipient 0xFF3E7D88647EBCDB
-----BEGIN PGP MESSAGE-----
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=pzkv
-----END PGP MESSAGE-----

Decryption

Decrypt the sample text by pasting it:

$ gpg --decrypt --armor
-----BEGIN PGP MESSAGE-----
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=pzkv
-----END PGP MESSAGE-----
gpg: encrypted with 4096-bit RSA key, ID 0x5912A795E90DD2CF, created
2016-05-24
      "Dr Duh <doc@duh.to>"

(Press Control-D)

Linux workstation 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux

Signing

Sign some sample text using the signing subkey:

$ echo "$(uname -a)" | gpg --armor --clearsign --default-key 0xBECFA3C1AE191D15
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Linux workstation 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux
-----BEGIN PGP SIGNATURE-----
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=+ylJ
-----END PGP SIGNATURE-----

Verifying signature

Verify the previous signature:

$ gpg
gpg: Go ahead and type your message ...
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Linux workstation 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux
-----BEGIN PGP SIGNATURE-----
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=+ylJ
-----END PGP SIGNATURE-----

(Press Control-D)

gpg: Signature made Wed 25 May 2016 00:00:00 AM UTC
gpg:                using RSA key 0xBECFA3C1AE191D15
gpg: Good signature from "Dr Duh <doc@duh.to>" [ultimate]
Primary key fingerprint: 011C E16B D45B 27A5 5BA8  776D FF3E 7D88 647E BCDB
     Subkey fingerprint: 07AA 7735 E502 C5EB E09E  B8B0 BECF A3C1 AE19 1D15

Putting it all together:

$ echo "$(uname -a)" | gpg --encrypt --sign --armor --default-key 0xFF3E7D88647EBCDB --recipient 0xBECFA3C1AE191D15 | gpg --decrypt --armor
gpg: encrypted with 4096-bit RSA key, ID 0x5912A795E90DD2CF, created 2016-05-24
      "Dr Duh <doc@duh.to>"
Linux workstation 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux
gpg: Signature made Wed 25 May 2016 01:00:00 AM UTC
gpg:                using RSA key 0xBECFA3C1AE191D15
gpg: Good signature from "Dr Duh <doc@duh.to>" [ultimate]
Primary key fingerprint: 011C E16B D45B 27A5 5BA8  776D FF3E 7D88 647E BCDB
     Subkey fingerprint: 07AA 7735 E502 C5EB E09E  B8B0 BECF A3C1 AE19 1D15

SSH

Update configuration

Paste the following text into a terminal window to create a recommended GPG agent configuration:

$ cat << EOF > ~/.gnupg/gpg-agent.conf
enable-ssh-support
pinentry-program /usr/bin/pinentry-curses
default-cache-ttl 60
max-cache-ttl 120
write-env-file
use-standard-socket
EOF

If you are using Linux on the desktop, you may want to use /usr/bin/pinentry-gnome3 to use a GUI manager.

Replace ssh-agent with gpg-agent

$ pkill ssh-agent ; pkill gpg-agent ; \
  eval $(gpg-agent --daemon --enable-ssh-support --use-standard-socket \
  --log-file ~/.gnupg/gpg-agent.log --write-env-file)

Copy public key to server

There is a -L option of ssh-add that lists public key parameters of all identities currently represented by the agent. Copy and paste the following output to the server authorized_keys file:

$ ssh-add -L
ssh-rsa AAAAB4NzaC1yc2EAAAADAQABAAACAz[...]zreOKM+HwpkHzcy9DQcVG2Nw== cardno:000605553211

Connect with public key authentication

$ ssh git@github.com -vvv
[...]
debug2: key: cardno:000605553211 (0x1234567890),
debug1: Authentications that can continue: publickey
debug3: start over, passed a different list publickey
debug3: preferred gssapi-keyex,gssapi-with-mic,publickey,keyboard-interactive,password
debug3: authmethod_lookup publickey
debug3: remaining preferred: keyboard-interactive,password
debug3: authmethod_is_enabled publickey
debug1: Next authentication method: publickey
debug1: Offering RSA public key: cardno:000605553211
debug3: send_pubkey_test
debug2: we sent a publickey packet, wait for reply
debug1: Server accepts key: pkalg ssh-rsa blen 535
debug2: input_userauth_pk_ok: fp e5:de:a5:74:b1:3e:96:9b:85:46:e7:28:53:b4:82:c3
debug3: sign_and_send_pubkey: RSA e5:de:a5:74:b1:3e:96:9b:85:46:e7:28:53:b4:82:c3
debug1: Authentication succeeded (publickey).
[...]

Troubleshooting

If you don't understand some option, read man gpg.
If you encounter problems connecting to YubiKey with GPG, simply try unplugging and re-inserting your YubiKey, and restarting the gpg-agent process.
If you receive the error, gpg: decryption failed: secret key not available - you likely need to install GnuPG version 2.x.
If you receive the error, Yubikey core error: no yubikey present - make sure the YubiKey is inserted correctly. It should blink once when plugged in.
If you still receive the error, Yubikey core error: no yubikey present - you likely need to install newer versions of yubikey-personalize as outlined in Install required software.
If you receive the error, Yubikey core error: write error - YubiKey is likely locked. Install and run yubikey-personalization-gui to unlock it.
If you receive the error, Key does not match the card's capability - you likely need to use 2048 bit RSA key sizes.
If you receive the error, sign_and_send_pubkey: signing failed: agent refused operation - you probably have ssh-agent running. Make sure you replaced ssh-agent with gpg-agent as noted above.
If you totally screw up, you can reset the card.