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I am aware of these documents: https://help.ubuntu.com/community/InstallCDCustomization http://blog.self.li/post/74294988486/creating-a-post-installation-script-for-ubuntu on making custom Ubuntu installation CD or DVD media. It's particularly clear on adding custom packages to the install.

But how can I customize user preferences, such as sleep timing or package update policy? I'd like to do this either as a custom installation CD, or at least as a click to execute script. The goal is to set up a bunch of machines, all with the same preferences settings.

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There are plenty programs that permit you do that. For me, one of the easiest one is remastersys.

1- Custom your Ubuntu with all the preference you want to have on the new iso.

2- Download remastersys. First you will need to add the repository:

vi /etc/apt/sources.list

# Remastersys
deb http://www.remastersys.klikit-linux.com/repository remastersys/

Save and exit. Run

 apt-get update

Install it

apt-get install remastersys

3- Now you just need to run to create the copy of your system:

sudo remastersys dist

This also lets you create backups on iso file, with the following command:

sudo remastersys backup nameyouwant.iso

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