Your question really cant be answered with specifics. You can use any software tool you want.
As for materials on building a ground control station for a UAV; I have not seen any though that does not mean there are not out there.
Lets face it, a UAV is just a fancy remote controlled airplane that has a greater range then the toy versions. UAVs that are in use today are controlled via a satellite connection and a much more advanced remote control unit.
I would say start with a search of this site and the internet if this is something you really are interested in.
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