fasttree: Approximately-maximum-likelihood phylogenetic trees from alignments

[Jason Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Tue Jan 16 22:03:02 2018 -0600
Changeset:	c2a282cbc6e8d805f88b804c74131ba55bf4bffe

Modified Files:
	Makefile
Added Files:
	fasttree/DESCR
	fasttree/Makefile
	fasttree/PLIST
	fasttree/TODO
	fasttree/distinfo
	fasttree/files/Makefile

Log Message:
fasttree: Approximately-maximum-likelihood phylogenetic trees from alignments

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=c2a282cbc6e8d805f88b804c74131ba55bf4bffe

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                |  1 +
 fasttree/DESCR          |  3 +++
 fasttree/Makefile       | 30 ++++++++++++++++++++++++++++++
 fasttree/PLIST          |  2 ++
 fasttree/TODO           |  2 ++
 fasttree/distinfo       |  6 ++++++
 fasttree/files/Makefile | 25 +++++++++++++++++++++++++
 7 files changed, 69 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 943009d90c..2f5ebbc04a 100644
--- a/Makefile
+++ b/Makefile
@@ -764,6 +764,7 @@ SUBDIR+=	fastjet
 SUBDIR+=	fastool
 SUBDIR+=	fastqc
 SUBDIR+=	fastrpc
+SUBDIR+=	fasttree
 SUBDIR+=	fbida
 SUBDIR+=	fbpager
 SUBDIR+=	fbpanel
diff --git a/fasttree/DESCR b/fasttree/DESCR
new file mode 100644
index 0000000000..fbc3d3f8cb
--- /dev/null
+++ b/fasttree/DESCR
@@ -0,0 +1,3 @@
+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.
diff --git a/fasttree/Makefile b/fasttree/Makefile
new file mode 100644
index 0000000000..daada82d88
--- /dev/null
+++ b/fasttree/Makefile
@@ -0,0 +1,30 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Tue Jan 16 21:48:02 CST 2018               #
+###########################################################
+
+DISTNAME=	FastTree-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	http://www.microbesonline.org/fasttree/
+EXTRACT_SUFX=	.c
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	http://www.microbesonline.org/fasttree/
+COMMENT=	Approximately-maximum-likelihood phylogenetic trees from alignments
+LICENSE=	gnu-gpl-v2
+
+WRKSRC=		${WRKDIR}
+
+CFLAGS=		-fopenmp
+
+PORTVERSION=	2.1.10
+
+INSTALLATION_DIRS=	bin
+
+do-extract:
+	${CP} ${DISTDIR}/${DISTFILES} ${WRKSRC}
+	${CP} ${FILESDIR}/Makefile ${WRKSRC}
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/fasttree/PLIST b/fasttree/PLIST
new file mode 100644
index 0000000000..58873d3872
--- /dev/null
+++ b/fasttree/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD$
+bin/FastTree
diff --git a/fasttree/TODO b/fasttree/TODO
new file mode 100644
index 0000000000..4ba83df5df
--- /dev/null
+++ b/fasttree/TODO
@@ -0,0 +1,2 @@
+
+FreeBSD: malloc -> aligned_alloc
diff --git a/fasttree/distinfo b/fasttree/distinfo
new file mode 100644
index 0000000000..50550aa375
--- /dev/null
+++ b/fasttree/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (FastTree-2.1.10.c) = 841905c09ce9fc7b133039682b9462ff62cf8219
+RMD160 (FastTree-2.1.10.c) = b9ba60c1c237e576086b163ed426f602dd34832d
+SHA512 (FastTree-2.1.10.c) = 36dcb8103c78cedf8432c5c1f47229290de41ef3099fe57e7f5c4facb657b43c85e99b5a576fa510f6245523643df2a428baf77c1118f60cfad77635919a39c1
+Size (FastTree-2.1.10.c) = 390916 bytes
diff --git a/fasttree/files/Makefile b/fasttree/files/Makefile
new file mode 100644
index 0000000000..ada070cda5
--- /dev/null
+++ b/fasttree/files/Makefile
@@ -0,0 +1,25 @@
+
+BIN =		FastTree
+SRC =		FastTree*.c
+CC ?=		gcc
+CFLAGS ?=	-O3
+CFLAGS +=	-DOPENMP -fopenmp -finline-functions -funroll-loops
+
+MKDIR ?=	mkdir
+INSTALL ?=	install
+PREFIX ?=	/usr/local
+DESTDIR ?=	.
+
+.PHONY:	all install clean
+
+all:	${BIN}
+
+${BIN}: ${SRC} Makefile
+	${CC} ${CFLAGS} ${SRC} -o ${BIN} -lm
+
+install: ${BIN}
+	${MKDIR} -p ${DESTDIR}${PREFIX}/bin
+	${INSTALL} -s -c ${BIN} ${DESTDIR}${PREFIX}/bin
+
+clean:
+	${RM} -f ${BIN}