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Mon, 18 Feb 2013 12:11:21 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1361189466.091646173edca5b62fc12d430879378d868ae45a.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/wgs-assembler/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/wgs-assembler/ChangeLog sci-biology/wgs-assembler/metadata.xml sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild X-VCS-Directories: sci-biology/wgs-assembler/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 091646173edca5b62fc12d430879378d868ae45a X-VCS-Branch: master Date: Mon, 18 Feb 2013 12:11:21 +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: 29ac3644-3343-42f1-9866-5eeae4f6920f X-Archives-Hash: 2fc2721f778ffccd1da3154b99165cb4 commit: 091646173edca5b62fc12d430879378d868ae45a Author: Justin Lecher gentoo org> AuthorDate: Mon Feb 18 12:11:06 2013 +0000 Commit: Justin Lecher gentoo org> CommitDate: Mon Feb 18 12:11:06 2013 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=09164617 newer version in the tree Signed-off-by: Justin Lecher gentoo.org> --- sci-biology/wgs-assembler/ChangeLog | 12 ---- sci-biology/wgs-assembler/metadata.xml | 9 --- sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild | 70 -------------------- 3 files changed, 0 insertions(+), 91 deletions(-) diff --git a/sci-biology/wgs-assembler/ChangeLog b/sci-biology/wgs-assembler/ChangeLog deleted file mode 100644 index 24fb71d..0000000 --- a/sci-biology/wgs-assembler/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/wgs-assembler -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*wgs-assembler-7.0 (27 Jan 2012) - - 27 Jan 2012; mmokrejs@fold.natur.cuni.cz +metadata.xml, - +wgs-assembler-7.0.ebuild: - sci-biology/wgs-assembler-7.0: version bump, would be nice if we could stop - compilation of the kmer/ subdir (an r1916 snapshot) and DEPEND on the external - http://kmer.sourceforge.net complete bundle instead - diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml deleted file mode 100644 index 3302123..0000000 --- a/sci-biology/wgs-assembler/metadata.xml +++ /dev/null @@ -1,9 +0,0 @@ - - - - - weaver@gentoo.org - Andrey Kislyuk - - sci-biology - diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild deleted file mode 100644 index b75a5b7..0000000 --- a/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/wgs-assembler-6.1.ebuild,v 1.3 2011/03/20 20:19:27 weaver Exp $ - -EAPI="2" - -inherit eutils toolchain-funcs - -DESCRIPTION="A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG" -HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/" -SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2" - -LICENSE="GPL-2" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -DEPEND="x11-libs/libXt - !x11-terms/terminator" -RDEPEND="${DEPEND} - app-shells/tcsh - dev-perl/Log-Log4perl" - -S="${WORKDIR}/wgs-${PV}" - -src_configure() { - sed -i -e "s/CC *= *gcc/CC = $(tc-getCC)/" \ - -e "s/CXX *= *g++/CXX = $(tc-getCXX)/" \ - "${S}"/src/c_make.as || die - sed -i -e "s/CC *:=.*/CC := $(tc-getCC)/" \ - -e "s/CXX *:=.*/CXX := $(tc-getCXX)/" \ - "${S}"/kmer/configure.sh || die - cd "${S}/kmer" - ./configure.sh || die -} - -src_compile() { - # not really an install target - emake -C kmer -j1 install || die - emake -C src -j1 SITE_NAME=LOCAL || die -} - -src_install() { - OSTYPE=$(uname) - MACHTYPE=$(uname -m) - MACHTYPE=${MACHTYPE/x86_64/amd64} - MY_S="${OSTYPE}-${MACHTYPE}" - sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die - - sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die - sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die - sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die - - dobin kmer/${MY_S}/bin/* || die - insinto /usr/$(get_libdir)/${PN} - doins kmer/${MY_S}/lib/* || die - # Collisions - # dolib.a kmer/${MY_S}/lib/* || die - insinto /usr/include/${PN} - doins kmer/${MY_S}/include/* - - insinto /usr/share/${PN} - doins -r ${MY_S}/bin/spec - insinto /usr/share/${PN}/lib - doins -r ${MY_S}/bin/TIGR || die - rm -rf ${MY_S}/bin/{TIGR,spec} - dobin ${MY_S}/bin/* || die - dolib.a ${MY_S}/lib/* || die - dodoc README -}