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I know some fragments of this question have been asked in previous posts and I have reviewed them - however I have a more thorough question...

I did not choose to do whole disk encryption when I used the alternative installer to install my 12.04 distro. I thought that truecypt worked with linux on system drive (whole disk) encryption - but sadly found out it did not.

I have totally tweaked and pimped out my installation and I do not want to have to go back and "install" to just get whole disk encryption. Any alternatives that anyone knows of?

I don't want just /home... I want the whole system installation protected and made secure so that when I boot I get a password to unencrypt.

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If you have another disk handy you can setup the encryption on the new disk and migrate everything over. dd can perform a bitwise transfer of everything to a new container, even one that has been encrypted.

If you just want to feel secure then you can use this how-to:

It does most of what you are asking and uses a password to decrypt root. To make it better you can use a usb stick for /boot and leave all of the root disk encrypted.

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