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Index: biology/Makefile
===================================================================
--- biology/Makefile
+++ biology/Makefile
@@ -96,6 +96,7 @@
SUBDIR += pycogent
SUBDIR += pyfasta
SUBDIR += python-nexus
+ SUBDIR += rainbow
SUBDIR += recombine
SUBDIR += ruby-bio
SUBDIR += rubygem-bio
Index: biology/rainbow/Makefile
===================================================================
--- /dev/null
+++ biology/rainbow/Makefile
@@ -0,0 +1,26 @@
+# $FreeBSD$
+
+PORTNAME= rainbow
+DISTVERSION= 2.0.4
+CATEGORIES= wip 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>
Index: biology/rainbow/distinfo
===================================================================
--- /dev/null
+++ biology/rainbow/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1520455667
+SHA256 (rainbow_2.0.4.tar.gz) = 79281aae3bccd1ad467afef6fc7c8327aaa8d56f538821e2833d2b8f26b5bafc
+SIZE (rainbow_2.0.4.tar.gz) = 77111
Index: biology/rainbow/files/patch-Makefile
===================================================================
--- /dev/null
+++ biology/rainbow/files/patch-Makefile
@@ -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
Index: biology/rainbow/pkg-descr
===================================================================
--- /dev/null
+++ biology/rainbow/pkg-descr
@@ -0,0 +1,3 @@
+Efficient tool for clustering and assembling short reads, especially for RAD.
+
+WWW: http://sourceforge.net/projects/bio-rainbow/

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