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I have a secondary storage drive thats partition like below.

Number  Start   End     Size    Type      File system  Flags
 1      1049kB  56.4GB  56.4GB  primary   ext4
 2      56.4GB  500GB   444GB   extended
 5      56.4GB  61.7GB  5369MB  logical   ext4
 6      61.7GB  500GB   438GB   logical   ext4

How do I safely shrink partition number 6 and reallocate the free space to partition number 1 without using a cd?

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Unmount the filesystems and then run gparted.
(Gparted is availabel as a normal package on most Linux distros so you don't need a live-CD.)

If you can't unmount there is no way you can do this safely.

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