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 22ADE138A1A for ; Sun, 8 Feb 2015 21:07:57 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 00C99E082B; Sun, 8 Feb 2015 21:07:54 +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 4D5A7E0871 for ; Sun, 8 Feb 2015 21:07:52 +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 1311134075D for ; Sun, 8 Feb 2015 21:07:51 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id C5E9711591 for ; Sun, 8 Feb 2015 21:07:47 +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: <1423254241.60ba53b88755c62f589c3787765bd6f39da78eef.ottxor@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/bowtie/bowtie-1.1.1.ebuild sci-biology/bowtie/bowtie-2.2.4.ebuild X-VCS-Directories: sci-biology/bowtie/ X-VCS-Committer: ottxor X-VCS-Committer-Name: Christoph Junghans X-VCS-Revision: 60ba53b88755c62f589c3787765bd6f39da78eef X-VCS-Branch: master Date: Sun, 8 Feb 2015 21:07:47 +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: ccc4c8ed-c911-416b-a4c3-6fabcb9aa0a6 X-Archives-Hash: bfa59fa9b3d44f8d9012972478999353 commit: 60ba53b88755c62f589c3787765bd6f39da78eef Author: Ted Tanberry gmail com> AuthorDate: Fri Feb 6 08:52:03 2015 +0000 Commit: Christoph Junghans gentoo org> CommitDate: Fri Feb 6 20:24:01 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=60ba53b8 Updated bowtie:{1,2} ebuilds to match current ebuild policy. --- sci-biology/bowtie/bowtie-1.1.1.ebuild | 29 +++++++++++++++++++---------- sci-biology/bowtie/bowtie-2.2.4.ebuild | 23 ++++++++++++----------- 2 files changed, 31 insertions(+), 21 deletions(-) diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild index ad20591..f152518 100644 --- a/sci-biology/bowtie/bowtie-1.1.1.ebuild +++ b/sci-biology/bowtie/bowtie-1.1.1.ebuild @@ -4,22 +4,27 @@ EAPI=5 -inherit base eutils toolchain-funcs +inherit eutils toolchain-funcs DESCRIPTION="An ultrafast memory-efficient short read aligner" HOMEPAGE="http://bowtie-bio.sourceforge.net/" -SRC_URI="mirror://sourceforge/bowtie-bio/bowtie-1.1.1-src.zip" +SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" LICENSE="Artistic" SLOT="1" -IUSE="" KEYWORDS="~amd64 ~x86 ~x64-macos" +IUSE="examples" + DEPEND="app-arch/unzip" RDEPEND="" PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch ) +src_prepare() { + epatch ${PATCHES[@]} +} + src_compile() { unset CFLAGS emake \ @@ -29,14 +34,18 @@ src_compile() { } src_install() { - dobin bowtie bowtie-* - exeinto /usr/share/${PN}/scripts - doexe scripts/* + dobin ${PN} ${PN}-* - insinto /usr/share/${PN} - doins -r genomes indexes + exeinto /usr/libexec/${PN} + doexe scripts/* - newman MANUAL bowtie.1 + newman MANUAL ${PN} dodoc AUTHORS NEWS TUTORIAL doc/README - dohtml doc/{manual.html,style.css} + docinto html + dodoc doc/{manual.html,style.css} + + if use examples; then + insinto /usr/share/${PN} + doins -r genomes indexes + fi } diff --git a/sci-biology/bowtie/bowtie-2.2.4.ebuild b/sci-biology/bowtie/bowtie-2.2.4.ebuild index 19e0bca..4b518ca 100644 --- a/sci-biology/bowtie/bowtie-2.2.4.ebuild +++ b/sci-biology/bowtie/bowtie-2.2.4.ebuild @@ -4,7 +4,7 @@ EAPI=5 -inherit base eutils toolchain-funcs +inherit eutils toolchain-funcs DESCRIPTION="An ultrafast memory-efficient short read aligner" HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/" @@ -12,9 +12,11 @@ SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source LICENSE="GPL-3" SLOT="2" -IUSE="examples" KEYWORDS="~amd64 ~x86" +IUSE="examples cpu_flags_x86_sse2" +REQUIRED_USE="cpu_flags_x86_sse2" + RDEPEND="dev-lang/perl" DEPEND="${RDEPEND} app-arch/unzip" @@ -23,16 +25,13 @@ S="${WORKDIR}/${PN}2-${PV}" PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch ) -pkg_pretend() { - grep "sse2" /proc/cpuinfo > /dev/null - if [[ $? -ne 0 ]] ; then - ewarn "Your processor does not support sse2. Bowtie will probably not work on this machine." - fi +src_prepare() { + epatch ${PATCHES[@]} } src_compile() { + unset CFLAGS emake \ - CC="$(tc-getCC)" \ CXX="$(tc-getCXX)" \ EXTRA_FLAGS="${LDFLAGS}" \ RELEASE_FLAGS="${CXXFLAGS} -msse2" @@ -40,12 +39,14 @@ src_compile() { src_install() { dobin ${PN}2 ${PN}2-* - exeinto /usr/share/${PN}2/scripts + + exeinto /usr/libexec/${PN}2 doexe scripts/* - newman MANUAL ${PN}2.1 + newman MANUAL ${PN}2.2 dodoc AUTHORS NEWS TUTORIAL - dohtml doc/manual.html doc/style.css + docinto html + dodoc doc/{manual.html,style.css} if use examples; then insinto /usr/share/${PN}2