svn commit: r466235 - in head/biology: . rainbow rainbow/files

[Jason W. Bacon]

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_${PORTVERSION}
+
+MAINTAINER=	jwb at FreeBSD.org
+COMMENT=	Efficient clustering and assembling of short reads, especially for RAD
+
+LICENSE=	GPLv3+
+
+USES=		gmake
+
+PLIST_FILES=	bin/rainbow bin/ezmsim bin/rbasm
+
+do-install:
+	@${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/