mlin/PhyloCSF

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SOURCE DISTRIBUTION

Please see our web site for more information about PhyloCSF and how to use it.
PhyloCSF is written in OCaml. This source distribution is divided into a
library, CamlPaml, containing generic infrastructure for phylogenetic rate
models, and a program implementing the PhyloCSF-specific models and driver
program. With additional development, the CamlPaml library will eventually be
released as a separate entity, but for now it is just part of this
distribution.

Here are the steps to build the source:

[1] Install the OCaml package manager OPAM

http://opam.ocamlpro.com/doc/Quick_Install.html

This will install a minimal OCaml toolchain (if not already present on your
system) and the OPAM package manager. Once it's installed, initialize your
shell environment by running: eval $(opam config env)

[2] Install dependencies using OPAM

opam install batteries gsl-ocaml twt

The gsl-ocaml package may require you to separately install the GNU Scientific
Library (GSL) from: http://www.gnu.org/software/gsl/
On Debian/Ubuntu systems GSL is available in the 'libgsl0-dev' package, and on
Mac OS X, 'gsl' is available in both Homebrew and MacPorts.

[3] Compile PhyloCSF

Now just run 'make' in this directory. This will build and install the
CamlPaml library, then compile the PhyloCSF executable and copy it to
PhyloCSF.ARCH in this directory, where e.g. ARCH = Linux.x86_64. This
executable should be usable by anyone on the same machine/cluster; they don't
have to set up OPAM or anything else.