Ubuntu – How to enable SOCKS 5 authentication in Network Proxy Preferences

A possible solution can be to use tsocks, an application that can redirect the network traffic through a socks proxy. Install tsocks package, modify /etc/tsocks.conf to set address and port number of your socks proxy, and run:

$ sudo -s
# tsocks apt-get update
# tsocks apt-get dist-upgrade
# exit
$

or

$ sudo -s
# . tsocks -on
# apt-get update
# apt-get dist-upgrade
# . tsocks -off # not really necessary, given the exit
# exit
$

You can think to a number of options, to simplify and automate its use.
Don't forget the leading dot, the Manpage has more deatails on this.

Edit: a shorter way to use it:

$ sudo tsocks apt-get update
$ sudo tsocks apt-get dist-upgrade

Go to /etc/apt. Create the file apt.conf if you don't have it there. Write the following lines there.

Acquire::http::proxy "http://username:password@proxyserver:port/";
Acquire::https::proxy "https://username:password@proxyserver:port/";
Acquire::socks::proxy "socks://username:password@proxyserver:port/";

Save it. You are done.