mlin/PhyloCSF

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|                 http://compbio.mit.edu/PhyloCSF                     | 
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SOURCE DISTRIBUTION

Please see our web site for more information about PhyloCSF. Compiling
this software from source may be difficult for most users, because it
requires an Objective Caml toolchain that's probably not already
present on your system. For this reason, we provide digitally-signed
32-bit and 64-bit Linux executables on our web site.

The 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:

[1A] Install various dependencies (Ubuntu 11.10+)

Install these packages using apt-get:
ocaml-findlib libocamlgsl-ocaml-dev libbatteries-ocaml-dev make

[1B] Install various dependencies (other Linux, Mac OS X)

- GNU Scientific Library 
* Objective Caml 3.11+, with native code compiler
* OCaml findlib
* OCaml Batteries Included 1.20+
* ocamlgsl 0.60+

* These can be set up using GODI: http://godi.camlcity.org/

[2] Configure OCaml findlib

If you installed findlib (OCaml's package manager) using the Ubuntu
packages, or any other method that led to system-wide installation, you
must set some environment variables to make it use a directory to which
you have write access. (Alternatively, you can complete the subsequent
steps as root, e.g. using sudo)

  mkdir -p $HOME/opt/lib/ocaml                     # or whatever
  export OCAMLPATH=$HOME/opt/lib/ocaml:$OCAMLPATH
  export OCAMLFIND_DESTDIR=$OCAMLPATH

To verify your configuration, run

  ocamlfind printconf

"Packages will be installed in" should be a directory you can write to,
and that same directory should appear in "Search path".

[3] Install ocaml+twt

The code is written in a dialect of OCaml for which you must install a
preprocessor from: http://people.csail.mit.edu/mikelin/ocaml+twt/
Download the tarball, extract it, and run

  make install INSTALLDIR=$HOME/directory/in/your/PATH
    -or-
  sudo make install

If you obtained this PhyloCSF source distribution by cloning the git
repository, ocaml+twt is available as a submodule. You can run

  git submodule init
  git submodule update
  cd twt

and then one of the above 'make install' commands.

[4] 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.