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.