You can use ./build.sh to configure and build with default options.

It is advised to run ./autogen.sh before ./configure (autoconf and automake
need to be installed on your system for autogen.sh to work)

./configure has an option named --with-cuda that allows you to specify
where your CUDA 6.5 toolkit is installed (usually /usr/local/cuda,
but some distros may have a different default location)

See README.txt