From c1fb3811426183133b6ee50bc58f03f2a90e93ca Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Sun, 8 May 2016 01:17:41 +0200
Subject: sci-biology/bwa: Version bump

Package-Manager: portage-2.2.28
---
 sci-biology/bwa/Manifest                        |  1 +
 sci-biology/bwa/bwa-0.7.13.ebuild               | 38 +++++++++++++++++++++++++
 sci-biology/bwa/files/bwa-0.7.13-Makefile.patch | 27 ++++++++++++++++++
 3 files changed, 66 insertions(+)
 create mode 100644 sci-biology/bwa/bwa-0.7.13.ebuild
 create mode 100644 sci-biology/bwa/files/bwa-0.7.13-Makefile.patch

(limited to 'sci-biology/bwa')

diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
index 9c0d995bfb1f..3cf0fb132cb5 100644
--- a/sci-biology/bwa/Manifest
+++ b/sci-biology/bwa/Manifest
@@ -1 +1,2 @@
 DIST bwa-0.7.12.tar.bz2 184599 SHA256 701dcad147ae470d741717a72c369b338df7f80bff4bb8eee8176c66f16d608c SHA512 3ea093b861c1596d20b1ee0336468b66e52bc9f26e3d0bcbba0ddccc7fe9b1af2c7e1ed2a4e1366fe93fec348152becc126d5f4685dae54f05e6c582488b3abd WHIRLPOOL 4b8651dedf2e09980850e7212fc2a77dc86b06f708af2077cff28cc843858b15825a203e3e02e7728418e9eb539004404f7c4b234c1f65de6a7b7dfe4dcfd1d0
+DIST bwa-0.7.13.tar.bz2 189670 SHA256 559b3c63266e5d5351f7665268263dbb9592f3c1c4569e7a4a75a15f17f0aedc SHA512 37966e914321d17b5a1d4e3a7786abdd9dd476e4dd7aaf924fb0e0726e3827a1414d9ffccc114a1a334943c8dde38273ce5fafdd1b429ab0f3cbf47ddbd6bedf WHIRLPOOL 86b278b301aa1ff4334c0d78709a61dc034895deb6aa2bd60ee45a595198343e7d60db458c61168b8c61a6ace21db394583b6314a56df3171a151f554c07f769
diff --git a/sci-biology/bwa/bwa-0.7.13.ebuild b/sci-biology/bwa/bwa-0.7.13.ebuild
new file mode 100644
index 000000000000..2ce3ff34f356
--- /dev/null
+++ b/sci-biology/bwa/bwa-0.7.13.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
+HOMEPAGE="http://bio-bwa.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+RDEPEND="dev-lang/perl"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-Makefile.patch
+)
+
+src_prepare() {
+	default
+	tc-export CC AR
+}
+
+src_install() {
+	dobin bwa
+
+	doman bwa.1
+
+	exeinto /usr/libexec/${PN}
+	doexe qualfa2fq.pl xa2multi.pl
+
+	dodoc NEWS.md README-alt.md README.md
+}
diff --git a/sci-biology/bwa/files/bwa-0.7.13-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.13-Makefile.patch
new file mode 100644
index 000000000000..39b437a02897
--- /dev/null
+++ b/sci-biology/bwa/files/bwa-0.7.13-Makefile.patch
@@ -0,0 +1,27 @@
+--- bwa-0.7.13/Makefile
++++ bwa-0.7.13/Makefile
+@@ -1,8 +1,8 @@
+-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
++AR?=			ar
+ DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
+ LOBJS=		utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
+ AOBJS=		QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
+@@ -26,10 +26,10 @@
+ all:$(PROG)
+ 
+ bwa:libbwa.a $(AOBJS) main.o
+-		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
++		$(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
+ 
+ bwamem-lite:libbwa.a example.o
+-		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
++		$(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
+ 
+ libbwa.a:$(LOBJS)
+ 		$(AR) -csru $@ $(LOBJS)
-- 
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