This revision of Caffe allows users to do the linear algebra with Eigen. For all the details of Caffe like documentation, installation instructions, etc., please refer to the original project site.
$ git checkout eigen
$ cp Makefile.config.example Makefile.config
# Uncomment USE_EIGEN := 1 in Makefile.config
$ make all
Enabling USE_EIGEN will set CPU_ONLY to 1 and omit BLAS settings.