Index: head/biology/mrbayes/files/patch-Makefile
===================================================================
--- head/biology/mrbayes/files/patch-Makefile	(revision 527482)
+++ head/biology/mrbayes/files/patch-Makefile	(nonexistent)
@@ -1,20 +0,0 @@
---- Makefile.orig	2005-12-22 11:13:06.000000000 -0500
-+++ Makefile	2014-08-15 12:36:02.000000000 -0400
-@@ -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)
-@@ -67,7 +67,7 @@
- 
- LIBS     +=   -lm
- 
--LDFLAGS  =   $(CFLAGS)
-+LDFLAGS  +=   $(CFLAGS)
- LDLIBS   =   $(LIBS)
- 
- OBJECTS   =   bayes.o command.o mbmath.o mcmc.o model.o plot.o sump.o sumt.o

Property changes on: head/biology/mrbayes/files/patch-Makefile
___________________________________________________________________
Deleted: fbsd:nokeywords
## -1 +0,0 ##
-yes
\ No newline at end of property
Deleted: svn:eol-style
## -1 +0,0 ##
-native
\ No newline at end of property
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: head/biology/mrbayes/Makefile
===================================================================
--- head/biology/mrbayes/Makefile	(revision 527482)
+++ head/biology/mrbayes/Makefile	(revision 527483)
@@ -1,31 +1,48 @@
 # Created by: mzaki@biol.s.u-tokyo.ac.jp
 # $FreeBSD$
 
 PORTNAME=	mrbayes
-PORTVERSION=	3.1.2
-PORTREVISION=	3
+DISTVERSIONPREFIX=	v
+DISTVERSION=	3.2.7
 CATEGORIES=	biology
-MASTER_SITES=	SF
 
-MAINTAINER=	mzaki@m.u-tokyo.ac.jp
+MAINTAINER=	mzaki@e-mail.ne.jp
 COMMENT=	Bayesian inference of phylogeny
 
-BROKEN=		unfetchable
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/COPYING
 
-OPTIONS_DEFINE=	EXAMPLES
+USES=		readline:port
+USE_GITHUB=	yes
+GH_ACCOUNT=	NBISweden
+GH_PROJECT=	MrBayes
 
-USES=		gmake readline:port
+GNU_CONFIGURE=	yes
 
-PLIST_FILES=	bin/mb
+OPTIONS_DEFINE=		DOCS EXAMPLES
+OPTIONS_DEFINE_amd64=	AVX FMA SSE
+OPTIONS_DEFINE_i386=	AVX FMA SSE
 
-PORTEXAMPLES=	adh.nex anolis.nex avian_ovomucoids.nex bglobin.nex \
-		cynmix.nex kim.nex primates.nex replicase.nex
+OPTIONS_DEFAULT_amd64=	SSE
 
-do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/mb ${STAGEDIR}${PREFIX}/bin/
-	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
-.for file in ${PORTEXAMPLES}
-	${INSTALL_DATA} ${WRKSRC}/${file} ${STAGEDIR}${EXAMPLESDIR}
-.endfor
+OPTIONS_RADIO=		MPI
+OPTIONS_RADIO_MPI=	MPICH OPENMPI
+
+OPTIONS_EXCLUDE_i386=	OPENMPI
+
+AVX_DESC=	Use AVX optimized routines
+FMA_DESC=	Use FMA optimized routines
+
+AVX_IMPLIES=		SSE
+AVX_CONFIGURE_OFF=	--disable-avx
+FMA_IMPLIES=		AVX SSE
+FMA_CONFIGURE_OFF=	--disable-fma
+MPICH_LIB_DEPENDS=	libmpich.so:net/mpich
+MPICH_CONFIGURE_ON=	--with-mpi
+MPICH_CONFIGURE_ENV=	CC="${LOCALBASE}/bin/mpicc"
+OPENMPI_LIB_DEPENDS=	libmpi.so:net/openmpi
+OPENMPI_CONFIGURE_ON=	--with-mpi
+OPENMPI_CONFIGURE_ENV=	CC="${LOCALBASE}/mpi/openmpi/bin/mpicc"
+SSE_CONFIGURE_OFF=	--disable-sse
 
 .include <bsd.port.mk>
Index: head/biology/mrbayes/distinfo
===================================================================
--- head/biology/mrbayes/distinfo	(revision 527482)
+++ head/biology/mrbayes/distinfo	(revision 527483)
@@ -1,2 +1,3 @@
-SHA256 (mrbayes-3.1.2.tar.gz) = c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4
-SIZE (mrbayes-3.1.2.tar.gz) = 545968
+TIMESTAMP = 1583009863
+SHA256 (NBISweden-MrBayes-v3.2.7_GH0.tar.gz) = 64da39c01f606d0413ce90a1dd3c1ce2cbdef4cbad99aee8a4b2391a2e8db244
+SIZE (NBISweden-MrBayes-v3.2.7_GH0.tar.gz) = 9825172
Index: head/biology/mrbayes/pkg-descr
===================================================================
--- head/biology/mrbayes/pkg-descr	(revision 527482)
+++ head/biology/mrbayes/pkg-descr	(revision 527483)
@@ -1,11 +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/
+WWW: http://nbisweden.github.io/MrBayes/
Index: head/biology/mrbayes/pkg-message
===================================================================
--- head/biology/mrbayes/pkg-message	(nonexistent)
+++ head/biology/mrbayes/pkg-message	(revision 527483)
@@ -0,0 +1,8 @@
+[
+{ type: install
+  message: <<EOM
+If MrBayes core dumps with "illegal hardware instruction (core dumped) mb", then
+it should be built on the target system.
+EOM
+}
+]

Property changes on: head/biology/mrbayes/pkg-message
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: head/biology/mrbayes/pkg-plist
===================================================================
--- head/biology/mrbayes/pkg-plist	(nonexistent)
+++ head/biology/mrbayes/pkg-plist	(revision 527483)
@@ -0,0 +1,15 @@
+bin/mb
+%%PORTDOCS%%%%DOCSDIR%%/COPYING
+%%PORTDOCS%%%%DOCSDIR%%/MBDating.pdf
+%%PORTDOCS%%%%DOCSDIR%%/Manual_MrBayes_v3.2.pdf
+%%PORTDOCS%%%%DOCSDIR%%/NEWS
+%%PORTDOCS%%%%DOCSDIR%%/README
+%%PORTDOCS%%%%DOCSDIR%%/hym.nex
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/avian_ovomucoids.nex
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/codon.nex
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cynmix.nex
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/finch.nex
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hymfossil.nex
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/primates.nex
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/replicase.nex
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sceloporus.nex

Property changes on: head/biology/mrbayes/pkg-plist
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property