From 565d0310d54ba529b128ffb34c33342e99bf6a15 Mon Sep 17 00:00:00 2001
From: Martin Wilke <miwi@FreeBSD.org>
Date: Sat, 15 Dec 2007 15:13:41 +0000
Subject: [PATCH] MrBayes is a program for the Bayesian estimation of
 phylogeny.

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.

WWW: http://mrbayes.csit.fsu.edu/

PR:		ports/118542
Submitted by:	mzaki at biol.s.u-tokyo.ac.jp
---
 biology/Makefile                     |  1 +
 biology/mrbayes/Makefile             | 34 ++++++++++++++++++++++++++++
 biology/mrbayes/distinfo             |  3 +++
 biology/mrbayes/files/patch-Makefile | 11 +++++++++
 biology/mrbayes/pkg-descr            | 11 +++++++++
 5 files changed, 60 insertions(+)
 create mode 100644 biology/mrbayes/Makefile
 create mode 100644 biology/mrbayes/distinfo
 create mode 100644 biology/mrbayes/files/patch-Makefile
 create mode 100644 biology/mrbayes/pkg-descr

diff --git a/biology/Makefile b/biology/Makefile
index 9cc884558da2..3b535a3b219f 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -46,6 +46,7 @@
     SUBDIR += migrate
     SUBDIR += molden
     SUBDIR += mopac
+    SUBDIR += mrbayes
     SUBDIR += mummer
     SUBDIR += nab
     SUBDIR += ncbi-toolkit
diff --git a/biology/mrbayes/Makefile b/biology/mrbayes/Makefile
new file mode 100644
index 000000000000..bb21910860d4
--- /dev/null
+++ b/biology/mrbayes/Makefile
@@ -0,0 +1,34 @@
+# New ports collection makefile for:	mrbayes
+# Date created:				11 December 2007
+# Whom:					mzaki@biol.s.u-tokyo.ac.jp
+#
+# $FreeBSD$
+#
+
+PORTNAME=	mrbayes
+PORTVERSION=	3.1.2
+CATEGORIES=	biology
+MASTER_SITES=	SF
+
+MAINTAINER=	mzaki@biol.s.u-tokyo.ac.jp
+COMMENT=	Bayesian inference of phylogeny
+
+USE_GMAKE=	yes
+
+LIB_DEPENDS+=	readline.5:${PORTSDIR}/devel/readline
+
+PLIST_FILES=	bin/mb
+
+PORTEXAMPLES=	adh.nex anolis.nex avian_ovomucoids.nex bglobin.nex \
+		cynmix.nex kim.nex primates.nex replicase.nex
+
+do-install:
+	@${INSTALL_PROGRAM} ${WRKSRC}/mb ${PREFIX}/bin/
+.if !defined(NOPORTEXAMPLES)
+	@${MKDIR} ${EXAMPLESDIR}
+.for file in ${PORTEXAMPLES}
+	@${INSTALL_DATA} ${WRKSRC}/${file} ${EXAMPLESDIR}
+.endfor
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/mrbayes/distinfo b/biology/mrbayes/distinfo
new file mode 100644
index 000000000000..c5a7efce9b6d
--- /dev/null
+++ b/biology/mrbayes/distinfo
@@ -0,0 +1,3 @@
+MD5 (mrbayes-3.1.2.tar.gz) = 942e4e0a90fa23481bb1f2e0fa0e0d66
+SHA256 (mrbayes-3.1.2.tar.gz) = c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4
+SIZE (mrbayes-3.1.2.tar.gz) = 545968
diff --git a/biology/mrbayes/files/patch-Makefile b/biology/mrbayes/files/patch-Makefile
new file mode 100644
index 000000000000..eb99e4b74905
--- /dev/null
+++ b/biology/mrbayes/files/patch-Makefile
@@ -0,0 +1,11 @@
+--- Makefile.orig	2005-12-23 01:13:06.000000000 +0900
++++ Makefile	2007-12-11 11:35:36.000000000 +0900
+@@ -19,7 +19,7 @@
+ 
+ # set compiler for the non-MPI version (mpicc will be used for the MPI
+ # version regardless of this setting)
+-CC = gcc
++CC ?= gcc
+ 
+ # set to yes if you want to use the readline library (make sure you have it
+ # installed on your machine)
diff --git a/biology/mrbayes/pkg-descr b/biology/mrbayes/pkg-descr
new file mode 100644
index 000000000000..11dff2bd39ca
--- /dev/null
+++ b/biology/mrbayes/pkg-descr
@@ -0,0 +1,11 @@
+MrBayes is a program for the Bayesian estimation of phylogeny.
+
+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.
+
+WWW: http://mrbayes.csit.fsu.edu/