Gentoo Installation Instructions

Most of the dependencies are available in Portage. You might want to install better performing linear algebra packages from the [science overlay](https://wiki.gentoo.org/wiki/Project:Science/Overlay; e.g. atlas. The sundials suite has changed its API somewhat. Until our mcmc code is changed to adapt to these changes, you should install version 2.7.0.

  # vfgen
  emerge dev-libs/mini-xml \
         sci-mathematics/ginac

  # MCMC
  USE="hl" emerge sci-libs/gsl \
         sci-libs/cblas-reference \
	 =sci-libs/sundials-2.7.0
	 
  # SBtab to hdf5
  emerge dev-libs/glib

The high level API of hdf5 is used by the sampler. So, it’s probably best to add it to the hdf5 USE flags.

Some of these packages might not have been declared stable. In this case you will have to add them to the package.accept_keywords file.

The MCMC solver uses the CVODES. solver for ODE model integration with forward sensitivity analysis.

As mentioned before, you might want to install atlas from the science overlay. If you do, you have to migrate to the science overlay eselect modules. Another alternative is sci-libs/gotoblas2 or sci-libs/openblas/, also from the science overlay.