Date: Mon, 2 Apr 2018 16:50:46 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r466235 - in head/biology: . rainbow rainbow/files Message-ID: <201804021650.w32GokP3064270@repo.freebsd.org>
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Author: jwb Date: Mon Apr 2 16:50:46 2018 New Revision: 466235 URL: https://svnweb.freebsd.org/changeset/ports/466235 Log: biology/rainbow: Efficient clustering and assembling of short reads Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14924 Added: head/biology/rainbow/ head/biology/rainbow/Makefile (contents, props changed) head/biology/rainbow/distinfo (contents, props changed) head/biology/rainbow/files/ head/biology/rainbow/files/patch-Makefile (contents, props changed) head/biology/rainbow/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Mon Apr 2 16:27:40 2018 (r466234) +++ head/biology/Makefile Mon Apr 2 16:50:46 2018 (r466235) @@ -96,6 +96,7 @@ SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus + SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio Added: head/biology/rainbow/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/rainbow/Makefile Mon Apr 2 16:50:46 2018 (r466235) @@ -0,0 +1,26 @@ +# $FreeBSD$ + +PORTNAME= rainbow +DISTVERSION= 2.0.4 +CATEGORIES= biology +MASTER_SITES= SF/bio-rainbow +DISTNAME= rainbow_${PORTVERSION} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Efficient clustering and assembling of short reads, especially for RAD + +LICENSE= GPLv3+ + +USES= gmake + +PLIST_FILES= bin/rainbow bin/ezmsim bin/rbasm + +do-install: + @${MKDIR} ${STAGEDIR}${PREFIX}/bin + ${INSTALL_PROGRAM} \ + ${WRKSRC}/rainbow \ + ${WRKSRC}/ezmsim \ + ${WRKSRC}/rbasm \ + ${STAGEDIR}${PREFIX}/bin + +.include <bsd.port.mk> Added: head/biology/rainbow/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/rainbow/distinfo Mon Apr 2 16:50:46 2018 (r466235) @@ -0,0 +1,3 @@ +TIMESTAMP = 1520455667 +SHA256 (rainbow_2.0.4.tar.gz) = 79281aae3bccd1ad467afef6fc7c8327aaa8d56f538821e2833d2b8f26b5bafc +SIZE (rainbow_2.0.4.tar.gz) = 77111 Added: head/biology/rainbow/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/rainbow/files/patch-Makefile Mon Apr 2 16:50:46 2018 (r466235) @@ -0,0 +1,10 @@ +--- Makefile.orig 2015-07-27 18:28:54 UTC ++++ Makefile +@@ -1,5 +1,5 @@ +-CC=gcc +-CFLAGS= -W -O2 -Wall -Wno-self-assign -Wno-unused-function ++CC?=gcc ++CFLAGS?= -W -O2 -Wall -Wno-self-assign -Wno-unused-function + DFLAGS= -D_FILE_OFFSET_BITS=64 + GLIBS=-lm + GENERIC_SRC= string.h bitvec.h file_reader.h hashset.h sort.h list.h dna.h heap.h stdaln.h vector.h Added: head/biology/rainbow/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/rainbow/pkg-descr Mon Apr 2 16:50:46 2018 (r466235) @@ -0,0 +1,10 @@ +Rainbow provides an ultra-fast and memory-efficient solution to clustering and +assembling short genetic sequence reads produced by Restriction site Associated +DNA Sequencing (RAD-seq). It does this by, first, clustering reads using a +spaced seed method, then it divides potential groups into haplotypes in a +top-down manner. Next, along a guide tree, it iteratively merges sibling +leaves in a bottom-up manner if they are similar enough. Finally, Rainbow uses +a greedy algorithm to locally assemble merged reads into contigs. Both optimal +and suboptimal assembly results are output. + +WWW: http://sourceforge.net/projects/bio-rainbow/
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