[gentoo-commits] proj/sci:master commit in: sci-biology/bwa/, sci-biology/bwa/files/

["Christoph Junghans" <ottxor@gentoo.org>]

commit:     b4649db619f8514efb9377422de3ea42154b3a80
Author:     Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Thu Feb  5 19:20:03 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Feb  5 19:20:03 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b4649db6

Updated bwa to 0.7.12 and modernized the build system. Removed hard-coded ar.

---
 sci-biology/bwa/bwa-0.7.12.ebuild        | 31 +++++++++++++++++++++++++++++++
 sci-biology/bwa/files/bwa_Makefile.patch | 27 +++++++++++++++++++++++++++
 sci-biology/bwa/metadata.xml             |  5 +++++
 3 files changed, 63 insertions(+)

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 0000000..353c4bf
--- /dev/null
+++ b/sci-biology/bwa/bwa-0.7.12.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit base 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}"/${PN}_Makefile.patch )
+
+src_compile() {
+	tc-export CC AR
+	default
+}
+
+src_install() {
+	dobin bwa || die
+	doman bwa.1 || die
+	exeinto /usr/share/${PN}
+	doexe qualfa2fq.pl xa2multi.pl || die
+	dodoc NEWS.md README-alt.md README.md || die
+}

diff --git a/sci-biology/bwa/files/bwa_Makefile.patch b/sci-biology/bwa/files/bwa_Makefile.patch
new file mode 100644
index 0000000..406e9b0
--- /dev/null
+++ b/sci-biology/bwa/files/bwa_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)

diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/bwa/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>