svn commit: r452595 - in head/biology: . iqtree

[Joseph Mingrone]

Author: jrm
Date: Sat Oct 21 16:57:53 2017
New Revision: 452595
URL: https://svnweb.freebsd.org/changeset/ports/452595

Log:
  New port, biology/iqtree: Efficient phylogenomic software
  
  WWW: http://www.iqtree.org/

Added:
  head/biology/iqtree/
  head/biology/iqtree/Makefile   (contents, props changed)
  head/biology/iqtree/distinfo   (contents, props changed)
  head/biology/iqtree/pkg-descr   (contents, props changed)
Modified:
  head/biology/Makefile

Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile	Sat Oct 21 16:35:56 2017	(r452594)
+++ head/biology/Makefile	Sat Oct 21 16:57:53 2017	(r452595)
@@ -37,6 +37,7 @@
     SUBDIR += hmmer
     SUBDIR += htslib
     SUBDIR += iolib
+    SUBDIR += iqtree
     SUBDIR += jalview
     SUBDIR += jellyfish
     SUBDIR += lagan

Added: head/biology/iqtree/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/iqtree/Makefile	Sat Oct 21 16:57:53 2017	(r452595)
@@ -0,0 +1,24 @@
+# $FreeBSD$
+
+PORTNAME=	iqtree
+DISTVERSIONPREFIX=	v
+DISTVERSION=	1.6.beta4
+CATEGORIES=	biology
+
+MAINTAINER=	jrm at FreeBSD.org
+COMMENT=	Efficient phylogenomic software by maximum likelihood
+
+LICENSE=	GPLv2
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+BUILD_DEPENDS=	${LOCALBASE}/libdata/pkgconfig/eigen3.pc:math/eigen3
+RUN_DEPENDS=	${LOCALBASE}/libdata/pkgconfig/eigen3.pc:math/eigen3
+
+USES=		cmake compiler:openmp
+USE_GITHUB=	yes
+GH_ACCOUNT=	Cibiv
+
+PLIST_FILES=	bin/iqtree example.cf example.nex example.phy models.nex
+WRKSRC=		${WRKDIR}/IQ-TREE-${DISTVERSION}
+
+.include <bsd.port.mk>

Added: head/biology/iqtree/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/iqtree/distinfo	Sat Oct 21 16:57:53 2017	(r452595)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1508602968
+SHA256 (Cibiv-iqtree-v1.6.beta4_GH0.tar.gz) = 78ff4cb03140aa36f5e057e0182f304e83f46cb729e09a1ef08ce9720bcce04f
+SIZE (Cibiv-iqtree-v1.6.beta4_GH0.tar.gz) = 4450460

Added: head/biology/iqtree/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/iqtree/pkg-descr	Sat Oct 21 16:57:53 2017	(r452595)
@@ -0,0 +1,15 @@
+IQ-TREE is efficient and versatile phylogenomic software, created as the
+successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE).  Development was
+motivated by the rapid accumulation of phylogenomic data, leading to a need for
+efficient phylogenomic software that can handle a large amount of data and
+provide more complex models of sequence evolution. To this end, IQ-TREE can
+utilize multicore computers and distributed parallel computing to speed up the
+analysis. IQ-TREE automatically performs checkpointing to resume an interrupted
+analysis.
+
+As input IQ-TREE accepts all common sequence alignment formats including PHYLIP,
+FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a self-readable
+report file (name suffix .iqtree), a NEWICK tree file (.treefile) which can be
+visualized by tree viewer programs such as FigTree, Dendroscope or iTOL.
+
+WWW: http://www.iqtree.org/