Date: Fri, 25 Sep 2015 18:34:29 +0000 (UTC) From: Ruslan Makhmatkhanov <rm@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r397848 - in head/biology: . fasttree Message-ID: <201509251834.t8PIYTsn080158@repo.freebsd.org>
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Author: rm Date: Fri Sep 25 18:34:29 2015 New Revision: 397848 URL: https://svnweb.freebsd.org/changeset/ports/397848 Log: FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. WWW: http://www.microbesonline.org/fasttree/ PR: 203295 Submitted by: Jason Bacon <jwbacon@tds.net> Added: head/biology/fasttree/ head/biology/fasttree/Makefile (contents, props changed) head/biology/fasttree/distinfo (contents, props changed) head/biology/fasttree/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Fri Sep 25 18:33:18 2015 (r397847) +++ head/biology/Makefile Fri Sep 25 18:34:29 2015 (r397848) @@ -20,6 +20,7 @@ SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastdnaml + SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += garlic Added: head/biology/fasttree/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/fasttree/Makefile Fri Sep 25 18:34:29 2015 (r397848) @@ -0,0 +1,33 @@ +# Created by: Jason Bacon <jwbacon@tds.net> +# $FreeBSD$ + +PORTNAME= FastTree +PORTVERSION= 2.1.8 +CATEGORIES= biology +MASTER_SITES= http://www.microbesonline.org/fasttree/ +EXTRACT_SUFX= .c + +MAINTAINER= jwbacon@tds.net +COMMENT= Approximately-maximum-likelihood phylogenetic trees from alignments + +# LICENSE= unspecified open source + +USES= compiler:openmp + +CFLAGS+= -DOPENMP -fopenmp -O3 -finline-functions -funroll-loops +LDFLAGS+= -lm + +PLIST_FILES= bin/FastTree + +do-extract: + ${MKDIR} ${WRKSRC} + ${CP} ${DISTDIR}/${DISTFILES} ${WRKSRC} + +do-build: + cd ${WRKSRC} && ${CC} ${CFLAGS} -o FastTree ${DISTFILES} ${LDFLAGS} + +do-install: + ${MKDIR} ${STAGEDIR}${PREFIX}/bin + ${INSTALL_PROGRAM} ${WRKSRC}/FastTree ${STAGEDIR}${PREFIX}/bin + +.include <bsd.port.mk> Added: head/biology/fasttree/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/fasttree/distinfo Fri Sep 25 18:34:29 2015 (r397848) @@ -0,0 +1,2 @@ +SHA256 (FastTree-2.1.8.c) = b172d160f1b12b764d21a6937c3ce01ba42fa8743d95e083e031c6947762f837 +SIZE (FastTree-2.1.8.c) = 385231 Added: head/biology/fasttree/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/fasttree/pkg-descr Fri Sep 25 18:34:29 2015 (r397848) @@ -0,0 +1,5 @@ +FastTree infers approximately-maximum-likelihood phylogenetic trees from +alignments of nucleotide or protein sequences. FastTree can handle alignments +with up to a million of sequences in a reasonable amount of time and memory. + +WWW: http://www.microbesonline.org/fasttree/
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