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I am currently using Ubuntu directly from the USB drive because I have problems with my hard drive. I would like to know how to backup my bootable USB drive after each use so that I can save files and programs without uploading them to a cloud service.

In other words, is there a way that I can save programs and/or files using the bootable USB if my hard drive is not usable?

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The feature you want is called Persistence.

If you want to make a new USB, with persistence:

Many Linux USB creators offer an option to enable Persistence.

In Ubuntu's USB creator:

Ubuntu's USB Creator - Persistence

And Unetbootin (Windows tool to create Linux bootable USBs):

Unetbootin

If you want to make your existing USB Persistent:

  1. Create an empty file called casper-rw in the USB's root using the disk-writing tool dd.

    dd if=/dev/zero of=/path/to/usb/casper-rw bs=2G count=1
    

    This will create 2 GB of storage for your files and programs. To increase it, modify the 2G in the command to increase. (For example, to get 4 GB of storage, 2G would be replaced with 4G)

    Replace /path/to/usb with the path to your USB (usually along the lines of /media/USERNAME/USB_NAME

  2. Make a filesystem on that file:

    mkfs.ext4 /path/to/usb/casper-rw
    
  3. Edit the boot/grub/grub.cfg file in your pen-drive's root. Look for the line starting with linux. Before the -- at the end, add persistent; so that the line's ending looks like: persistent --.

Now whatever changes you make, they'll be saved.

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