From 0419b171c90990250e722a251c682a5040ab86a6 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Tue, 3 Mar 2015 15:17:11 +0000 Subject: [PATCH] Version BUmp; thanks Ted Tanberry Package-Manager: portage-2.2.17/cvs/Linux x86_64 Manifest-Sign-Key: 0xB9D4F231BD1558AB! --- sci-biology/bwa/ChangeLog | 11 ++++-- sci-biology/bwa/Manifest | 27 +++++++++++---- sci-biology/bwa/bwa-0.7.12.ebuild | 34 +++++++++++++++++++ .../bwa/files/bwa-0.7.12-Makefile.patch | 27 +++++++++++++++ 4 files changed, 90 insertions(+), 9 deletions(-) create mode 100644 sci-biology/bwa/bwa-0.7.12.ebuild create mode 100644 sci-biology/bwa/files/bwa-0.7.12-Makefile.patch 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 +bwa-0.7.12.ebuild, + +files/bwa-0.7.12-Makefile.patch: + Version BUmp; thanks Ted Tanberry 11 Mar 2013; Justin Lecher metadata.xml: Drop Andrey as maintainer so that bugs get assigned to sci-biology directly @@ -63,4 +69,3 @@ 26 Feb 2009; Andrey Kislyuk +metadata.xml, +bwa-0.4.5.ebuild: New package, ebuild written by me. - diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest index fa60b1f3df34..c4b32f0d5740 100644 --- a/sci-biology/bwa/Manifest +++ b/sci-biology/bwa/Manifest @@ -1,21 +1,36 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA512 +AUX bwa-0.7.12-Makefile.patch 911 SHA256 b67d36d5fe755f572cf8b5998e5dedc0545e89aa6eb7ca808327f06f592c132a SHA512 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/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) -- 2.26.2