I don't believe that there is anything in most standard packages (debian, fedora, ubuntu) that will do it, but check out the last post in this thread on the ubuntu forums: https://ubuntuforums.org/showthread.php?t=892381 It has a link to a google code project called 'cryptmanager' which apparently does what you want. I think it is in python, so it shouldn't be too insane to install (hopefully).
During Ubuntu installation you are asked if you want to encrypt your home folder (and therefore sub-folders in it as well) so it is possible. Exactly how to do it after installation I have no idea but Ubuntuforums will have someone there who can advise you I'm sure. You don't specify which Linux you are using but I'm fairly sure the encryption is available across all distros.