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I'm using docky in Ubuntu 11.10 with gnome-shell and sometimes the notifications cover the dock. It would be great if the position of the notifications can be changed.

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There is a tweaking tool just for this purpose. However, it seems to involve installing a different version of notify-osd. This is from the link above:

Install the patched (configurable) NotifyOSD in Ubuntu 11.10 or 11.04:

sudo add-apt-repository ppa:leolik/leolik 
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install libnotify-bin
pkill notify-osd

Install NotifyOSD Config:

sudo add-apt-repository ppa:nilarimogard/webupd8
sudo apt-get update
sudo apt-get install notifyosdconfig
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