Now mirnylib and hiclib are actually pip-installable! (hiclib even installs mirnylib from "tip" automatically). I tried to declare dependencies in the mirnylib and hiclib installers based on what 3rd party libraries are imported explicitly (e.g., pysam is only a dependency for hiclib).
The platform-specific caveats should be put in the README file. I basically said that you should have the HDF5 shared libraries already installed, and that you to already have a working basic scientific python stack (numpy/scipy/matplotlib) installed before installing this.
I have decided to leave out numpy/scipy/matplotlib from the install_requires list. On some platforms numpy and scipy ships with the system Python, but is located in a nonstandard place (not in site-packages), which means that a pip install could cause collisions and mess things up.