INSTALL

INSTALLATION
============

The primary documentation for DART is on biowiki.org. This includes
the installation instructions, a detailed and hyperlinked version of
which may be found here:
http://biowiki.org/BuildingDART

However, the brief version goes like this:

Type the following...

	./configure
	make all

...to make all targets.

Alternatively, the following will make individual packages:

	make xrate
	make handel
	make stemloc
	make evoldoer
	make protpal

You are strongly advised NOT to use parallel make, as it
probably will not work.

Executables go in the following directories:

	dart/bin
	dart/perl

Some programs expect you to set the environment variable DARTDIR
to the root path of the dart distribution, but omitting this
is rarely fatal.

To compile, you'll need the following tools:

  -- GNU gcc  (version 4.0 or higher)
  -- GNU make (probably any recent version, but 3.80 is safe)
  -- GNU ar   (found in the binutils package; version 2.14 is safe)
  -- GNU test/rm/mv/ln       (found in the coreutils package)

You may be able to get away without having GNU ar, but probably not
without GNU make and definitely not without GNU gcc.


CAVEATS WITH THE CONFIGURE SCRIPT
=================================

The configure script is somewhat subfunctional; it does not currently
implement all autoconf options correctly (for example, it does not
yet allow building object files outside the main source directory).


OPTIONAL DEPENDENCIES
=====================

There are several optional packages that can be installed to extend
the features of DART. The configuration script will automatically look
for these features, or you can show it where to look using
command-line options.

The packages are:
- hmmoc (Gerton Lunter's Hidden Markov Model Compiler)
- guile (the GNU Scheme extension language)
- libhmsbeagle (fast computation of phylogenetic likelihoods using GPUs)

For full details of the roles of these packages in DART and the
command-line options required to clue in the 'configure' script on
where to find them, see the main installation page:

http://biowiki.org/BuildingDart