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The Arduino Yun runs a derivative of OpenWrt called Linino. The Linino project actually builds AllJoyn packages that can be installed. They are current with the 14.02 release.

You can find the latest version of the Linino firmware here:

The AllJoyn packages can be found here:

With the latest Linino firmware installed, you can simply do the following steps to install these package if your Arduino Yun has access to the Internet.

opkg update
opkg install alljoyn alljoyn-config alljoyn-notification ...

If you prefer the web UI, go into the advanced settings on your Yun, then select the "System" tab and under that select the "Software" tab. Partway down, you will see what looks like a grayed out tab called "Available". Click on that then make sure that you are in the "A's" and you should see the AllJoyn Packages and be able to install them from there.

You may need to restart the Arduino Yun for the alljoyn-daemon to be started.