Version BUmp; thanks Ted Tanberry

(Portage version: 2.2.17/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

3 files changed, 69 insertions, 3 deletions

diff --git a/sci-biology/bwa/ChangeLog b/sci-biology/bwa/ChangeLog
index fceee193618e..c5a829a1850d 100644
--- a/sci-biology/bwa/ChangeLog
+++ b/sci-biology/bwa/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/bwa
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/ChangeLog,v 1.13 2013/03/11 14:54:24 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/ChangeLog,v 1.14 2015/03/03 15:17:10 jlec Exp $
+
+*bwa-0.7.12 (03 Mar 2015)
+
+  03 Mar 2015; Justin Lecher <jlec@gentoo.org> +bwa-0.7.12.ebuild,
+  +files/bwa-0.7.12-Makefile.patch:
+  Version BUmp; thanks Ted Tanberry
 
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
@@ -63,4 +69,3 @@
   26 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml,
   +bwa-0.4.5.ebuild:
   New package, ebuild written by me.
-
diff --git a/sci-biology/bwa/bwa-0.7.12.ebuild b/sci-biology/bwa/bwa-0.7.12.ebuild
new file mode 100644
index 000000000000..d035ad395945
--- /dev/null
+++ b/sci-biology/bwa/bwa-0.7.12.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/bwa-0.7.12.ebuild,v 1.1 2015/03/03 15:17:10 jlec Exp $
+
+EAPI=5
+
+inherit eutils 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/${P}.tar.bz2"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+PATCHES=( "${FILESDIR}"/${P}-Makefile.patch )
+
+src_prepare() {
+	epatch ${PATCHES[@]}
+	tc-export CC AR
+}
+
+src_install() {
+	dobin bwa
+
+	doman bwa.1
+
+	exeinto /usr/libexec/${PN}
+	doexe qualfa2fq.pl xa2multi.pl
+
+	dodoc NEWS.md README-alt.md README.md
+}
diff --git a/sci-biology/bwa/files/bwa-0.7.12-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.12-Makefile.patch
new file mode 100644
index 000000000000..406e9b052376
--- /dev/null
+++ b/sci-biology/bwa/files/bwa-0.7.12-Makefile.patch
@@ -0,0 +1,27 @@
+--- Makefile
++++ 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)