Attachment 165067 Details for Bug 205890 – biology_phyml.diff

[patch] biology_phyml.diff

biology_phyml.diff (text/plain), 5.44 KB, created by tkato432 on 2016-01-04 18:31:06 UTC

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Creator: tkato432

Created: 2016-01-04 18:31:06 UTC

Size: 5.44 KB

patch

obsolete

>diff -urN /usr/ports/biology/phyml/Makefile biology/phyml/Makefile
>--- /usr/ports/biology/phyml/Makefile	2015-08-24 04:08:16.018908000 +0900
>+++ biology/phyml/Makefile	2016-01-05 00:00:00.000000000 +0900
>@@ -2,31 +2,59 @@
> # $FreeBSD: head/biology/phyml/Makefile 375747 2014-12-28 19:14:13Z bapt $
> 
> 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>
>diff -urN /usr/ports/biology/phyml/distinfo biology/phyml/distinfo
>--- /usr/ports/biology/phyml/distinfo	2015-08-24 04:08:16.029767000 +0900
>+++ biology/phyml/distinfo	2016-01-05 00:00:00.000000000 +0900
>@@ -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 -urN /usr/ports/biology/phyml/pkg-descr biology/phyml/pkg-descr
>--- /usr/ports/biology/phyml/pkg-descr	2015-08-24 04:08:16.041887000 +0900
>+++ biology/phyml/pkg-descr	2016-01-05 00:00:00.000000000 +0900
>@@ -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/

Flags:

vlad-fbsd: maintainer-approval+

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Attachments on bug 205890: 165067