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To prepare an ubuntu system to compile the application: sudo apt-get install git autogen automake g++ libftdi-dev To bootstrap the build system: ./autogen.sh This will generate the configure string and various autotools dependencies. Then, to compile a linux binary ("papilio-prog"): ./configure && make Or to generate a windows binary ("papilio-prog.exe"): ./configure --host=i686-w64-mingw32 --build=i686-linux && make That is assuming you have MinGW installed. On Debian and Ubuntu systems, "apt-get mingw64" should be all that's needed. The windows binary will still need the FTDI driver DLL installed on the system to work.