Date: Sat, 21 Oct 2017 16:57:53 +0000 (UTC) From: Joseph Mingrone <jrm@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r452595 - in head/biology: . iqtree Message-ID: <201710211657.v9LGvroM053225@repo.freebsd.org>
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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@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/
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