svn commit: r397848 - in head/biology: . fasttree

[Ruslan Makhmatkhanov]

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 at 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 at tds.net>
+# $FreeBSD$
+
+PORTNAME=	FastTree
+PORTVERSION=	2.1.8
+CATEGORIES=	biology
+MASTER_SITES=	http://www.microbesonline.org/fasttree/
+EXTRACT_SUFX=	.c
+
+MAINTAINER=	jwbacon at 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/