Find Boost when installed in an architecture-specific directory (e.g. /usr/lib/x86_64-linux-gnu), achieved by updating to (slightly tweaked) latest versions of axboost* from the autoconf extensions repository (https://www.gnu.org/software/autoconf-archive)
Find Eigen3, including when it is installed to /usr/include/eigen3
Use C++03 standard explicitly (g++-8 defaults to c++14, but Cufflinks doesn't compile with modern standards due to name clashes)
Use boost::unordered, not boost::tr1, which has been removed as of recent releases of Boost.
/usr/lib/x86_64-linux-gnu), achieved by updating to (slightly tweaked) latest versions of axboost* from the autoconf extensions repository (https://www.gnu.org/software/autoconf-archive)