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

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

[Christoph Junghans]

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>

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

[Justin Lecher]

commit:     de8eb4ef90bedc116258edad0d769d7469dbc28c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar  3 15:16:58 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar  3 15:16:58 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=de8eb4ef

IMport to CVS

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/bwa/bwa-0.7.12.ebuild        | 34 --------------------------------
 sci-biology/bwa/files/bwa_Makefile.patch | 27 -------------------------
 sci-biology/bwa/metadata.xml             |  5 -----
 3 files changed, 66 deletions(-)

diff --git a/sci-biology/bwa/bwa-0.7.12.ebuild b/sci-biology/bwa/bwa-0.7.12.ebuild
deleted file mode 100644
index 62488f3..0000000
--- a/sci-biology/bwa/bwa-0.7.12.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-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}"/${PN}_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_Makefile.patch b/sci-biology/bwa/files/bwa_Makefile.patch
deleted file mode 100644
index 406e9b0..0000000
--- a/sci-biology/bwa/files/bwa_Makefile.patch
+++ /dev/null
@@ -1,27 +0,0 @@
---- 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
deleted file mode 100644
index f17a827..0000000
--- a/sci-biology/bwa/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-biology</herd>
-</pkgmetadata>

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

[Martin Mokrejs]

commit:     71c08006931ce9a56edaa201c603d40933498021
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Feb 28 20:04:03 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Feb 28 20:04:03 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=71c08006

sci-biology/bwa: version bump; added a note about a brach of bwa-0.7.13 which has alternative Apache2 license

Package-Manager: portage-2.2.26

 sci-biology/bwa/bwa-0.7.13.ebuild               | 36 +++++++++++++++++++++++++
 sci-biology/bwa/files/bwa-0.7.13-Makefile.patch | 27 +++++++++++++++++++
 sci-biology/bwa/metadata.xml                    | 11 ++++++++
 3 files changed, 74 insertions(+)

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 0000000..27f314b
--- /dev/null
+++ b/sci-biology/bwa/bwa-0.7.13.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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/${P}.tar.bz2"
+
+LICENSE="GPL-3"
+# bwa-0.7.13 has "Apache2" branch with Apache2-licensed BWA with ropebwt2 index
+# feature which is slower than "bwtsw" algorithm but it has a permissive license.
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+PATCHES=( "${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-0.7.13-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.13-Makefile.patch
new file mode 100644
index 0000000..406e9b0
--- /dev/null
+++ b/sci-biology/bwa/files/bwa-0.7.13-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..ceb43ea
--- /dev/null
+++ b/sci-biology/bwa/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="sourceforge">bio-bwa</remote-id>
+  </upstream>
+</pkgmetadata>

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

[David Seifert]

commit:     7f516dcc0ff31783264d5aa43b598564d6dd5d1a
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep  2 08:11:47 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep  2 08:11:47 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f516dcc

sci-biology/bwa: Latest in main tree

 sci-biology/bwa/bwa-0.7.16.ebuild               | 36 -------------------------
 sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 -------------------
 sci-biology/bwa/metadata.xml                    | 11 --------
 3 files changed, 74 deletions(-)

diff --git a/sci-biology/bwa/bwa-0.7.16.ebuild b/sci-biology/bwa/bwa-0.7.16.ebuild
deleted file mode 100644
index 1568adff3..000000000
--- a/sci-biology/bwa/bwa-0.7.16.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-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/${P}.tar.bz2"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-RDEPEND="dev-lang/perl"
-
-DOCS=( NEWS.md README-alt.md README.md )
-PATCHES=( "${FILESDIR}"/${PN}-0.7.15-Makefile.patch )
-
-src_configure() {
-	tc-export CC AR
-	default
-}
-
-src_install() {
-	dobin bwa
-
-	doman bwa.1
-
-	exeinto /usr/libexec/${PN}
-	doexe qualfa2fq.pl xa2multi.pl
-
-	einstalldocs
-}

diff --git a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
deleted file mode 100644
index 39b437a02..000000000
--- a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
+++ /dev/null
@@ -1,27 +0,0 @@
---- 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)

diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml
deleted file mode 100644
index ceb43ead2..000000000
--- a/sci-biology/bwa/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">bio-bwa</remote-id>
-  </upstream>
-</pkgmetadata>

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

[Aisha Tammy]

commit:     14015a59ac70cd4a572b88a5be07718db566b62a
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Tue Sep 22 11:05:21 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Sep 22 11:05:21 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=14015a59

sci-biology/bwa: drop package

present in ::gentoo

Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 sci-biology/bwa/bwa-0.7.17.ebuild               | 34 -------------------------
 sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 --------------------
 sci-biology/bwa/metadata.xml                    | 11 --------
 3 files changed, 72 deletions(-)

diff --git a/sci-biology/bwa/bwa-0.7.17.ebuild b/sci-biology/bwa/bwa-0.7.17.ebuild
deleted file mode 100644
index 429ba43e6..000000000
--- a/sci-biology/bwa/bwa-0.7.17.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-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}"/${PN}-0.7.15-Makefile.patch )
-DOCS=( NEWS.md README-alt.md README.md )
-
-src_configure() {
-	tc-export CC AR
-}
-
-src_install() {
-	dobin bwa
-
-	exeinto /usr/libexec/${PN}
-	doexe qualfa2fq.pl xa2multi.pl
-
-	einstalldocs
-	doman bwa.1
-}

diff --git a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
deleted file mode 100644
index 39b437a02..000000000
--- a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
+++ /dev/null
@@ -1,27 +0,0 @@
---- 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)

diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml
deleted file mode 100644
index ceb43ead2..000000000
--- a/sci-biology/bwa/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">bio-bwa</remote-id>
-  </upstream>
-</pkgmetadata>