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I'm currently running a Linux Ubuntu installation on my laptop, and we are doing CTF's at school so I need to have Kali available.

However, I also need to customize my Kali (for preference) so I want to be using a USB with a saved installation of Kali. When I tried installing it, it said that it was the only Debian installation on the system, and was wondering if I wanted to save the GRUB-loader on master (HD ?). I was very unsure what to do so I said no for safety of my Ubuntu installation. However when I restarted it wouldn't load Kali.

Do I save GRUB on the same hard disk on which the Ubuntu installation is (the one inside the laptop)? Or should it be on the USB stick with the rest of the Kali installation? If so, what might I be doing wrong.

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Essentially, what you're looking for is called persistence. UNetbootin supports it for Ubuntu, I believe, but for Kali you're going to need to set it up manually.

First things first, if you're installing to a flash drive, don't touch the GRUB installation on your main linux install.

This article takes you through the steps of installation, summarized here:

1) Set up your USB with Kali, using a Kali iso. The first step in the guide has a link to an article detailing the steps.

2) Create a new partition on the drive alongside the existing Kali install

3) Create an ext3 file system on the partition

mkfs.ext3 -L persistence /dev/sdb3
e2label /dev/sdb3 persistence

4) Create the config file that is used to enable persistence, and set a mount point

mkdir -p /mnt/my_usb
mount /dev/sdb3 /mnt/my_usb
echo "/ union" > /mnt/my_usb/persistence.conf
umount /dev/sdb3

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