Import rainbow-2.0.4 as wip/rainbow.

[Jason Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed May 11 10:46:58 2016 -0500
Changeset:	e037a06e0d5439c736e00edfa047e11d5bbd1037

Added Files:
	rainbow/DESCR
	rainbow/Makefile
	rainbow/PLIST
	rainbow/TODO
	rainbow/distinfo
	rainbow/patches/patch-Makefile

Log Message:
Import rainbow-2.0.4 as wip/rainbow.

Short reads clustering and local assembly.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=e037a06e0d5439c736e00edfa047e11d5bbd1037

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 rainbow/DESCR                  |  1 +
 rainbow/Makefile               | 40 ++++++++++++++++++++++++++++++++++++++++
 rainbow/PLIST                  |  4 ++++
 rainbow/TODO                   |  1 +
 rainbow/distinfo               |  7 +++++++
 rainbow/patches/patch-Makefile | 12 ++++++++++++
 6 files changed, 65 insertions(+)

diffs:
diff --git a/rainbow/DESCR b/rainbow/DESCR
new file mode 100644
index 0000000..459ae9d
--- /dev/null
+++ b/rainbow/DESCR
@@ -0,0 +1 @@
+Short reads clustering and local assembly.
diff --git a/rainbow/Makefile b/rainbow/Makefile
new file mode 100644
index 0000000..0ba1560
--- /dev/null
+++ b/rainbow/Makefile
@@ -0,0 +1,40 @@
+# $NetBSD$
+#
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+DISTNAME=	rainbow_${PORTVERSION}
+PKGNAME=	rainbow-${PORTVERSION}
+CATEGORIES=	biology
+# FreeBSD MASTER_SITES: SF/bio-rainbow
+MASTER_SITES=	${MASTER_SITE_SOURCEFORGE:=bio-rainbow/}
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	http://sourceforge.net/projects/bio-rainbow/
+COMMENT=	Short reads clustering and local assembly
+# LICENSE=	unspecified
+
+# Test and change if necessary.
+# MAKE_JOBS_SAFE=	no
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	gmake
+
+PORTVERSION=	2.0.4
+DATADIR=	${PREFIX}/share/rainbow
+DOCSDIR=	${PREFIX}/share/doc/rainbow
+
+INSTALLATION_DIRS=	bin
+
+do-install:
+	${INSTALL_PROGRAM} \
+		${WRKSRC}/rainbow \
+		${WRKSRC}/ezmsim \
+		${WRKSRC}/rbasm \
+		${DESTDIR}${PREFIX}/bin
+
+# Linux doesn't have zlib in the base, so just in case...
+# .include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/rainbow/PLIST b/rainbow/PLIST
new file mode 100644
index 0000000..467a882
--- /dev/null
+++ b/rainbow/PLIST
@@ -0,0 +1,4 @@
+@comment $NetBSD$
+bin/ezmsim
+bin/rainbow
+bin/rbasm
diff --git a/rainbow/TODO b/rainbow/TODO
new file mode 100644
index 0000000..b687356
--- /dev/null
+++ b/rainbow/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/rainbow/distinfo b/rainbow/distinfo
new file mode 100644
index 0000000..086405e
--- /dev/null
+++ b/rainbow/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (rainbow_2.0.4.tar.gz) = c8a8458892873f59136176a3960f337ee7bea376
+RMD160 (rainbow_2.0.4.tar.gz) = bec9fa59563a06fd274b531acd33060b7c5c6a21
+SHA512 (rainbow_2.0.4.tar.gz) = 4308b618cc87811f3fcaabe508304a3df80de3c0c7b667d235db1ed336531517c9764a1af402cfe7dc3339ec903f9fb868d0a7f092c27fa579e74a635694cae9
+Size (rainbow_2.0.4.tar.gz) = 77111 bytes
+SHA1 (patch-Makefile) = e57277fb2ec920881718a211b415299bb16d26c6
diff --git a/rainbow/patches/patch-Makefile b/rainbow/patches/patch-Makefile
new file mode 100644
index 0000000..101f4e7
--- /dev/null
+++ b/rainbow/patches/patch-Makefile
@@ -0,0 +1,12 @@
+$NetBSD$
+
+--- 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