From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id F260D1396D0 for ; Sat, 2 Sep 2017 08:12:04 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 6F146E0B4B; Sat, 2 Sep 2017 08:12:04 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 415DEE0B4B for ; Sat, 2 Sep 2017 08:12:04 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 2F444341665 for ; Sat, 2 Sep 2017 08:12:03 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id D068E8B1E for ; Sat, 2 Sep 2017 08:12:01 +0000 (UTC) From: "David Seifert" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "David Seifert" Message-ID: <1504339907.7f516dcc0ff31783264d5aa43b598564d6dd5d1a.soap@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-0.7.16.ebuild sci-biology/bwa/files/bwa-0.7.15-Makefile.patch sci-biology/bwa/metadata.xml X-VCS-Directories: sci-biology/bwa/files/ sci-biology/bwa/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 7f516dcc0ff31783264d5aa43b598564d6dd5d1a X-VCS-Branch: master Date: Sat, 2 Sep 2017 08:12:01 +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: 6e7cbc0a-cfd9-44fb-9673-01b8c8122772 X-Archives-Hash: d81f1864d6f91fa1e1394cb4e6dc9857 commit: 7f516dcc0ff31783264d5aa43b598564d6dd5d1a Author: David Seifert gentoo org> AuthorDate: Sat Sep 2 08:11:47 2017 +0000 Commit: David Seifert gentoo 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 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - - bio-bwa - -