ports/118542: New port: biology/mrbayes Bayesian inference of phylogeny

[Motomichi Matsuzaki]

>Number:         118542
>Category:       ports
>Synopsis:       New port: biology/mrbayes Bayesian inference of phylogeny
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Tue Dec 11 03:00:07 UTC 2007
>Closed-Date:
>Last-Modified:
>Originator:     Motomichi Matsuzaki
>Release:        
>Organization:
>Environment:
>Description:
MrBayes is a program for the Bayesian estimation of phylogeny.
>How-To-Repeat:

>Fix:


Patch attached with submission follows:

# This is a shell archive.  Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file".  Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
#	biology/mrbayes
#	biology/mrbayes/Makefile
#	biology/mrbayes/distinfo
#	biology/mrbayes/pkg-descr
#	biology/mrbayes/files
#	biology/mrbayes/files/patch-Makefile
#
echo c - biology/mrbayes
mkdir -p biology/mrbayes > /dev/null 2>&1
echo x - biology/mrbayes/Makefile
sed 's/^X//' >biology/mrbayes/Makefile << 'END-of-biology/mrbayes/Makefile'
X# New ports collection makefile for:	mrbayes
X# Date created:				11 December 2007
X# Whom:					mzaki at biol.s.u-tokyo.ac.jp
X#
X# $FreeBSD$
X#
X
XPORTNAME=	mrbayes
XPORTVERSION=	3.1.2
XCATEGORIES=	biology
XMASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
XMASTER_SITE_SUBDIR=	${PORTNAME}
X
XMAINTAINER=	mzaki at biol.s.u-tokyo.ac.jp
XCOMMENT=	Bayesian inference of phylogeny
X
XUSE_GMAKE=	yes
X
XLIB_DEPENDS=    readline.5:${PORTSDIR}/devel/readline
X
XPLIST_FILES=	bin/mb
X
XPORTEXAMPLES=	adh.nex anolis.nex avian_ovomucoids.nex bglobin.nex \
X		cynmix.nex kim.nex primates.nex replicase.nex
X
Xdo-install:
X	@${INSTALL_PROGRAM} ${WRKSRC}/mb ${PREFIX}/bin/
X.if !defined(NOPORTEXAMPLES)
X	@${MKDIR} ${EXAMPLESDIR}
X.for file in ${PORTEXAMPLES}
X	@${INSTALL_DATA} ${WRKSRC}/${file} ${EXAMPLESDIR}
X.endfor
X.endif
X
X.include <bsd.port.mk>
END-of-biology/mrbayes/Makefile
echo x - biology/mrbayes/distinfo
sed 's/^X//' >biology/mrbayes/distinfo << 'END-of-biology/mrbayes/distinfo'
XMD5 (mrbayes-3.1.2.tar.gz) = 942e4e0a90fa23481bb1f2e0fa0e0d66
XSHA256 (mrbayes-3.1.2.tar.gz) = c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4
XSIZE (mrbayes-3.1.2.tar.gz) = 545968
END-of-biology/mrbayes/distinfo
echo x - biology/mrbayes/pkg-descr
sed 's/^X//' >biology/mrbayes/pkg-descr << 'END-of-biology/mrbayes/pkg-descr'
XMrBayes is a program for the Bayesian estimation of phylogeny.
X
XBayesian inference of phylogeny is based upon a quantity called the
Xposterior probability distribution of trees, which is the probability of a
Xtree conditioned on the observations. The conditioning is accomplished
Xusing Bayes's theorem. The posterior probability distribution of trees is
Ximpossible to calculate analytically; instead, MrBayes uses a simulation
Xtechnique called Markov chain Monte Carlo (or MCMC) to approximate the
Xposterior probabilities of trees.
X
XWWW: http://mrbayes.csit.fsu.edu/
END-of-biology/mrbayes/pkg-descr
echo c - biology/mrbayes/files
mkdir -p biology/mrbayes/files > /dev/null 2>&1
echo x - biology/mrbayes/files/patch-Makefile
sed 's/^X//' >biology/mrbayes/files/patch-Makefile << 'END-of-biology/mrbayes/files/patch-Makefile'
X--- Makefile.orig	2005-12-23 01:13:06.000000000 +0900
X+++ Makefile	2007-12-11 11:35:36.000000000 +0900
X@@ -19,7 +19,7 @@
X 
X # set compiler for the non-MPI version (mpicc will be used for the MPI
X # version regardless of this setting)
X-CC = gcc
X+CC ?= gcc
X 
X # set to yes if you want to use the readline library (make sure you have it
X # installed on your machine)
END-of-biology/mrbayes/files/patch-Makefile
exit



>Release-Note:
>Audit-Trail:
>Unformatted: