If you have no notification, you must watch your Terminal every doing long progress command such as apt-get update. But if there is notification, you can leave your Terminal, do another task, and let the system notifies if your command has been finished. There is a program to do it is undistract-me.
Install undistract-meOpen your Terminal and perform this command
sudo apt-get install undistract-meNote: this undistract-me package is available starting from Ubuntu Trusty until Wily. You can't execute command undistract-me, because that is basically just package which install some shell scripts. You must do the configuration to make it works.
The ConfigurationCopy these two lines into your ~/.bashrc file. Make sure it looks like picture below.
source /usr/share/undistract-me/long-running.bash notify_when_long_running_commands_finish_install
Then source it by this command:
source ~/.bashrcExplanation: first line does source long-running.bash file, then second line executes a function inside long-running.bash which makes the notification appears. The last source command is important to make sure bash program recognize the new configuration (so you don't need to restart the Terminal window).