OpenOCD (Open On-Chip Debugger) is open-source software that interfaces with the Flyswatter2. OpenOCD provides debugging and in-system programming for embedded target devices. You will need to compile OpenOCD from source, and patch the source with one of the OpenOCD Patches for Flyswatter 2 support.
Whichever guide you use, be sure to install the patch! Both guides include instructions on downloading and installing the patch.
Compiling OpenOCD Linux - This set of instructions uses libFTDI, an open-source driver library for FTDI devices.