Date: Fri, 26 Feb 2016 13:03:05 +0000 (UTC) From: Wen Heping <wen@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r409605 - head/biology/phyml Message-ID: <201602261303.u1QD35As068660@repo.freebsd.org>
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Author: wen Date: Fri Feb 26 13:03:05 2016 New Revision: 409605 URL: https://svnweb.freebsd.org/changeset/ports/409605 Log: - Update to 3.2.0 - Update pkg-descr PR: 205890 Submitted by: tkato432@yahoo.com Modified: head/biology/phyml/Makefile head/biology/phyml/distinfo head/biology/phyml/pkg-descr Modified: head/biology/phyml/Makefile ============================================================================== --- head/biology/phyml/Makefile Fri Feb 26 12:56:36 2016 (r409604) +++ head/biology/phyml/Makefile Fri Feb 26 13:03:05 2016 (r409605) @@ -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= ${WRKSRC}/src +USE_GITHUB= yes +GH_ACCOUNT= stephaneguindon -USES= autoreconf +USES= autoreconf libtool pkgconfig GNU_CONFIGURE= yes +CONFIGURE_ARGS= --disable-beagle -PLIST_FILES= bin/phyml +PORTDOCS= * +PORTEXAMPLES= * +PLIST_FILES= bin/phyml${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" + +.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> Modified: head/biology/phyml/distinfo ============================================================================== --- head/biology/phyml/distinfo Fri Feb 26 12:56:36 2016 (r409604) +++ head/biology/phyml/distinfo Fri Feb 26 13:03:05 2016 (r409605) @@ -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 Modified: head/biology/phyml/pkg-descr ============================================================================== --- head/biology/phyml/pkg-descr Fri Feb 26 12:56:36 2016 (r409604) +++ head/biology/phyml/pkg-descr Fri Feb 26 13:03:05 2016 (r409605) @@ -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/
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