wip/bwa: import bwa-0.7.17

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

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed Dec 13 16:33:19 2017 -0600
Changeset:	8d9fcbf56785a255f9edd5bfc989025ca795e83a

Added Files:
	bwa/DESCR
	bwa/Makefile
	bwa/PLIST
	bwa/distinfo
	bwa/patches/patch-Makefile

Log Message:
wip/bwa: import bwa-0.7.17

BWA is a software package for mapping low-divergent sequences against a large
reference genome, such as the human genome.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=8d9fcbf56785a255f9edd5bfc989025ca795e83a

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

diffstat:
 bwa/DESCR                  |  2 ++
 bwa/Makefile               | 32 ++++++++++++++++++++++++++++++++
 bwa/PLIST                  |  1 +
 bwa/distinfo               |  7 +++++++
 bwa/patches/patch-Makefile | 15 +++++++++++++++
 5 files changed, 57 insertions(+)

diffs:
diff --git a/bwa/DESCR b/bwa/DESCR
new file mode 100644
index 0000000000..1a8e65be4a
--- /dev/null
+++ b/bwa/DESCR
@@ -0,0 +1,2 @@
+BWA is a software package for mapping low-divergent sequences against a large
+reference genome, such as the human genome.
diff --git a/bwa/Makefile b/bwa/Makefile
new file mode 100644
index 0000000000..8226f45a16
--- /dev/null
+++ b/bwa/Makefile
@@ -0,0 +1,32 @@
+# $NetBSD: Makefile,v 1.4 2016/07/09 06:37:51 wiz Exp $
+#
+
+DISTNAME=	bwa-0.7.17
+CATEGORIES=	biology
+GITHUB_TAG=     v${PKGVERSION_NOREV}
+MASTER_SITES=	${MASTER_SITE_GITHUB:=lh3/}
+#EXTRACT_SUFX=	.tar.bz2
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	http://bio-bwa.sourceforge.net/
+COMMENT=	Map low-divergent sequences against a large reference genome
+LICENSE=	gnu-gpl-v3
+
+USE_TOOLS+=	perl:run gmake
+REPLACE_PERL=	*.pl
+
+INSTALLATION_DIRS=	bin ${PKGMANDIR}/man1
+
+# unconditionally uses <emmintrin.h>
+ONLY_FOR_PLATFORM=	*-*-x86_64 *-*-i386 *-*-ia64
+
+CFLAGS.SunOS+=	-Du_int32_t=uint32_t
+LDFLAGS.SunOS+=	-lsocket -lnsl
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/bwa ${DESTDIR}${PREFIX}/bin
+	${INSTALL_SCRIPT} ${WRKSRC}/*.pl ${DESTDIR}${PREFIX}/bin
+	${INSTALL_MAN} ${WRKSRC}/*.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/bwa/PLIST b/bwa/PLIST
new file mode 100644
index 0000000000..48d96a5493
--- /dev/null
+++ b/bwa/PLIST
@@ -0,0 +1 @@
+@comment $NetBSD$
diff --git a/bwa/distinfo b/bwa/distinfo
new file mode 100644
index 0000000000..ea2867dfc6
--- /dev/null
+++ b/bwa/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (bwa-0.7.17.tar.gz) = 77f9aac723110227ea51cb42011336d291d03723
+RMD160 (bwa-0.7.17.tar.gz) = d26a266387dee4fc9fcf6eef4f7ffcc076495c22
+SHA512 (bwa-0.7.17.tar.gz) = 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48
+Size (bwa-0.7.17.tar.gz) = 232593 bytes
+SHA1 (patch-Makefile) = 8ed885e6d9b37f1ece5a725c57955ee79f74a1fe
diff --git a/bwa/patches/patch-Makefile b/bwa/patches/patch-Makefile
new file mode 100644
index 0000000000..0e7a61be88
--- /dev/null
+++ b/bwa/patches/patch-Makefile
@@ -0,0 +1,15 @@
+$NetBSD: patch-Makefile,v 1.1 2015/12/12 16:56:04 wiedi Exp $
+
+Don't overwrite pkgsrc CC and CFLAGS
+
+--- Makefile.orig	2014-05-19 13:11:41 UTC
++++ Makefile
+@@ -1,6 +1,6 @@
+-CC=			gcc
++CC?=			gcc
+ #CC=			clang --analyze
+-CFLAGS=		-g -Wall -Wno-unused-function -O2
++CFLAGS?=		-g -Wall -Wno-unused-function -O2
+ WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
+ AR=			ar
+ DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)