From 13463a6f0171da354ad056ffd7aca4cc002c0f0f Mon Sep 17 00:00:00 2001
From: Pjotr Prins <pjotr.public01@thebird.nl>
Date: Thu, 5 Jun 2008 13:35:45 +0000
Subject: [PATCH] MrBayes - a biology package for phylogeny

svn path=/nixpkgs/trunk/; revision=11986
---
 .../science/biology/mrbayes/builder.sh        |  9 +++++++++
 .../science/biology/mrbayes/default.nix       | 20 +++++++++++++++++++
 2 files changed, 29 insertions(+)
 create mode 100644 pkgs/applications/science/biology/mrbayes/builder.sh
 create mode 100644 pkgs/applications/science/biology/mrbayes/default.nix

diff --git a/pkgs/applications/science/biology/mrbayes/builder.sh b/pkgs/applications/science/biology/mrbayes/builder.sh
new file mode 100644
index 00000000000..5b3a54946fc
--- /dev/null
+++ b/pkgs/applications/science/biology/mrbayes/builder.sh
@@ -0,0 +1,9 @@
+# builder for mrbayes - note: only builds on Unix
+
+source $stdenv/setup
+
+tar xvfz $src
+cd mrbayes-*
+make
+mkdir -p $out/bin
+cp -v mb $out/bin
diff --git a/pkgs/applications/science/biology/mrbayes/default.nix b/pkgs/applications/science/biology/mrbayes/default.nix
new file mode 100644
index 00000000000..78295faf69a
--- /dev/null
+++ b/pkgs/applications/science/biology/mrbayes/default.nix
@@ -0,0 +1,20 @@
+{stdenv, fetchurl, readline}:
+
+stdenv.mkDerivation rec {
+  # FIXME: replace Makefile so we can build MPI & MAC support
+
+  name = "mrbayes-3.1.2";
+  src = fetchurl {
+    url = "mirror://sourceforge/mrbayes/${name}.tar.gz";
+    sha256 = "1x7j8ca5wjrqrxmcpvd375ydm3s2pbkzykv8xfhg1jc037g560n6";
+  };
+  builder = ./builder.sh;
+  buildInputs = [readline];
+
+  meta = {
+    description     = "Bayesian Inference of Phylogeny";
+    longDescription = ''Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.'';
+    license     = "GPL2";
+    homepage    = http://mrbayes.csit.fsu.edu/;
+  };
+}