Requirements

First install the packages ecryptfs-utils and rsync:

# apt-get install ecryptfs-utils rsync lsof

Then load the ecryptfs kernel module:

# modprobe ecryptfs

And make it permanent in /etc/modules-load.d/modules.conf.

Assisted Encrypted Home Directory

The user whose home directory you want to encrypt MUST NOT be logged in. For example, you can be logged as root in a tty.

Then run as root:

# ecryptfs-migrate-home -u <username>

When this is done the user must login BEFORE rebooting the computer.

If the user can access the files in the users home directory you can remove the backup folder in /home/<username>.<random characters>

The user should also run this command to get the random encryption key and store it in a secure location (outside the encrypted home directory and not on the same machine) in case a recovery is needed:

ecryptfs-unwrap-passphrase

Assisted Encrypted Swap Partition

To encrypt the swap partition too:

# apt-get install cryptsetup
# ecryptfs-setup-swap