- Update to 3.2.0

- Update pkg-descr

PR:		205890
Submitted by:	tkato432@yahoo.com

3 files changed, 62 insertions, 34 deletions

diff --git a/biology/phyml/Makefile b/biology/phyml/Makefile
index d5f3d9ed2293..4d512f5145dc 100644
--- a/biology/phyml/Makefile
+++ b/biology/phyml/Makefile
@@ -2,31 +2,59 @@
 # $FreeBSD$
 
 PORTNAME=	phyml
-PORTVERSION=	20121109
+DISTVERSIONPREFIX=	v
+DISTVERSION=	3.2.0
+PORTEPOCH=	1
 CATEGORIES=	biology
-MASTER_SITES=	GOOGLE_CODE
-DISTNAME=	${PORTNAME}-20120412
-DIST_SUBDIR=	${PORTNAME}
-
-PATCH_SITES=	${MASTER_SITES}
-PATCHFILES=	${PORTVERSION}.patch
-PATCH_DIST_STRIP=	-p4
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Simple, fast, and accurate algorithm to estimate large phylogenies
 
 LICENSE=	GPLv2
+LICENSE_FILE=	${WRKSRC}/COPYING
 
-PATCH_WRKSRC=	${WRKSRC}/src
+USE_GITHUB=	yes
+GH_ACCOUNT=	stephaneguindon
 
-USES=		autoreconf
+USES=		autoreconf libtool pkgconfig
 GNU_CONFIGURE=	yes
+CONFIGURE_ARGS=	--disable-beagle
+
+PORTDOCS=	*
+PORTEXAMPLES=	*
+PLIST_FILES=	bin/phyml${BIN_SUFFIX}
+
+OPTIONS_DEFINE=		DOCS EXAMPLES
+OPTIONS_RADIO=		MPI
+OPTIONS_RADIO_MPI=	MPICH2 OPENMPI
+
+MPICH2_LIB_DEPENDS=	libmpich.so:${PORTSDIR}/net/mpich2
+MPICH2_MAKE_ARGS=	CC="${LOCALBASE}/bin/mpicc"
+OPENMPI_LIB_DEPENDS=	libmpi.so:${PORTSDIR}/net/openmpi
+OPENMPI_MAKE_ARGS=	CC="${LOCALBASE}/mpi/openmpi/bin/mpicc"
 
-PLIST_FILES=	bin/phyml
+.include <bsd.port.options.mk>
+
+.if ${PORT_OPTIONS:MMPICH2} || ${PORT_OPTIONS:MOPENMPI}
+CONFIGURE_ARGS+=	--enable-mpi
+BIN_SUFFIX=		-mpi
+.else
+CONFIGURE_ARGS+=	--disable-mpi
+BIN_SUFFIX=		# none
+.endif
 
 post-patch:
 	@${REINPLACE_CMD} -e \
-		'/^AC_INIT/s|,esyscmd.*,|,[${PORTVERSION}],| ; \
-		 s|-O2 -msse|$${CFLAGS}|' ${WRKSRC}/configure.ac
+		's|-O2 .* $${ARCH_flag}|$${CFLAGS}|' ${WRKSRC}/configure.ac
+
+post-install-DOCS-on:
+	@${MKDIR} ${STAGEDIR}${DOCSDIR}
+	(cd ${WRKSRC}/doc && ${INSTALL_DATA} *.pdf \
+		${STAGEDIR}${DOCSDIR})
+
+post-install-EXAMPLES-on:
+	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
+	@(cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . \
+		${STAGEDIR}${EXAMPLESDIR})
 
 .include <bsd.port.mk>
diff --git a/biology/phyml/distinfo b/biology/phyml/distinfo
index c588175155a7..c8d91b69279d 100644
--- a/biology/phyml/distinfo
+++ b/biology/phyml/distinfo
@@ -1,4 +1,2 @@
-SHA256 (phyml/phyml-20120412.tar.gz) = a43e51534a1ae2d1ee4c94ced3a1855813ff4872a6c9c2b83b369ddb71198417
-SIZE (phyml/phyml-20120412.tar.gz) = 4089133
-SHA256 (phyml/20121109.patch) = 3aa8bebd0ff78a553795ddda512ef1c7542d1e3c90c1da61c7125c304f6caa2c
-SIZE (phyml/20121109.patch) = 11016
+SHA256 (stephaneguindon-phyml-v3.2.0_GH0.tar.gz) = 9fec8fc26e69cad8d58bf2c9433b531754e4f026dc3464d07958b6c824783fde
+SIZE (stephaneguindon-phyml-v3.2.0_GH0.tar.gz) = 1239843
diff --git a/biology/phyml/pkg-descr b/biology/phyml/pkg-descr
index 4e2aa57579c7..221eaa774c84 100644
--- a/biology/phyml/pkg-descr
+++ b/biology/phyml/pkg-descr
@@ -1,18 +1,20 @@
-PhyML is a software that estimates maximum likelihood phylogenies from 
-alignments of nucleotide or amino acid sequences. It provides a wide range of
-options that were designed to facilitate standard phylogenetic analyses. The
-main strengths of PhyML lies in the large number of substitution models coupled
-to various options to search the space of phylogenetic tree topologies, going
-from very fast and efficient methods to slower but generally more accurate
-approaches. It also implements two methods to evaluate branch supports in a
-sound statistical framework (the non-parametric bootstrap and the approximate
-likelihood ratio test). PhyML was designed to process moderate to large data
-sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long
-can analyzed. In practice however, the amount of memory required to process a
-data set is proportional of the product of the number of sequences by their
-length. Hence, a large number of sequences can only be processed provided that
-they are short. Also, PhyML can handle long sequences provided that they are
-not numerous. With most standard personal computers, the "comfort zone" for
-PhyML generally lies around 3 to 500 sequences less than 2,000 character long.
+PhyML is a software that estimates maximum likelihood phylogenies from
+alignments of nucleotide or amino acid sequences. It provides a wide
+range of options that were designed to facilitate standard phylogenetic
+analyses. The main strengths of PhyML lies in the large number of
+substitution models coupled to various options to search the space of
+phylogenetic tree topologies, going from very fast and efficient methods
+to slower but generally more accurate approaches. It also implements two
+methods to evaluate branch supports in a sound statistical framework
+(the non-parametric bootstrap and the approximate likelihood ratio
+test). PhyML was designed to process moderate to large data sets. In
+theory, alignments with up to 4,000 sequences 2,000,000 character-long
+can analyzed. In practice however, the amount of memory required to
+process a data set is proportional of the product of the number of
+sequences by their length. Hence, a large number of sequences can only
+be processed provided that they are short. Also, PhyML can handle long
+sequences provided that they are not numerous. With most standard
+personal computers, the "comfort zone" for PhyML generally lies around 3
+to 500 sequences less than 2,000 character long.
 
-WWW: http://code.google.com/p/phyml/
+WWW: https://github.com/stephaneguindon/phyml/