From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 9E9C0138AD0 for ; Sun, 8 Feb 2015 21:07:50 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 229C2E079B; Sun, 8 Feb 2015 21:07:50 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 59B15E0782 for ; Sun, 8 Feb 2015 21:07:49 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 20C043406CF for ; Sun, 8 Feb 2015 21:07:48 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id AFA391157C for ; Sun, 8 Feb 2015 21:07:46 +0000 (UTC) From: "Christoph Junghans" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Christoph Junghans" Message-ID: <1423164003.b4649db619f8514efb9377422de3ea42154b3a80.ottxor@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/bwa/, sci-biology/bwa/files/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/bwa/bwa-0.7.12.ebuild sci-biology/bwa/files/bwa_Makefile.patch sci-biology/bwa/metadata.xml X-VCS-Directories: sci-biology/bwa/files/ sci-biology/bwa/ X-VCS-Committer: ottxor X-VCS-Committer-Name: Christoph Junghans X-VCS-Revision: b4649db619f8514efb9377422de3ea42154b3a80 X-VCS-Branch: master Date: Sun, 8 Feb 2015 21:07:46 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: caa59121-18c4-418c-855f-855d463c2080 X-Archives-Hash: 8f2cf733714d26bbb35b05362854d7a6 commit: b4649db619f8514efb9377422de3ea42154b3a80 Author: Ted Tanberry gmail com> AuthorDate: Thu Feb 5 19:20:03 2015 +0000 Commit: Christoph Junghans gentoo 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 @@ + + + + sci-biology +