commit: 215a7570a21fb795331b069f13560156fbad4e76 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Mon Sep 21 19:31:30 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Mon Sep 21 19:31:30 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=215a7570
sci-biology/wgs-assembler: Use new python eclass Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild | 78 ---------------------- .../wgs-assembler/wgs-assembler-8.3_rc2.ebuild | 17 ++--- 2 files changed, 6 insertions(+), 89 deletions(-) diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild deleted file mode 100644 index 5f4b775..0000000 --- a/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild +++ /dev/null @@ -1,78 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -PYTHON_DEPEND=2 - -inherit eutils python toolchain-funcs - -DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler also known as 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" -KEYWORDS="~amd64 ~x86" -IUSE="static-libs" - -DEPEND=" - x11-libs/libXt - !x11-terms/terminator" -RDEPEND="${DEPEND} - app-shells/tcsh - dev-perl/Log-Log4perl" - -S="${WORKDIR}/wgs-${PV}" - -pkg_setup() { - python_set_active_version 2 - python_pkg_setup -} - -src_prepare() { - # epatch \ - # "${FILESDIR}"/${P}-build.patch - tc-export CC CXX -} - -src_configure() { - cd "${S}/kmer" - ./configure.sh || die -} - -src_compile() { - # not really an install target - emake -C kmer -j1 install - emake -C src -j1 SITE_NAME=LOCAL -} - -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/* - insinto /usr/"$(get_libdir)/${PN}" - use static-libs && doins kmer/"${MY_S}"/lib/* - - insinto /usr/include/"${PN}" - doins kmer/"${MY_S}"/include/* - - insinto /usr/share/"${PN}"/lib - doins -r "${MY_S}"/bin/TIGR - rm -rf "${MY_S}"/bin/TIGR || die - dobin "${MY_S}"/bin/* - use static-libs && dolib.a "${MY_S}"/lib/* - dodoc README - - # avoid file collision - rm -f "${D}"/usr/bin/jellyfish -} diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild index 9b481a2..e1b5585 100644 --- a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild +++ b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild @@ -4,15 +4,15 @@ EAPI=5 -PYTHON_DEPEND=2 +PYTHON_COMPAT=( python2_7 ) -inherit eutils python toolchain-funcs +inherit eutils python-single-r1 toolchain-funcs MY_PV="${PV/_}" # convert from _rc2 to rc2 -DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler also known as Celera Assembler and CABOG" +DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler (Celera Assembler and CABOG)" HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"; -SRC_URI="http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.3/wgs-${MY_PV}.tar.bz2"; +SRC_URI="http://sourceforge.net/projects/${PN}/files/${PN}/wgs-8.3/wgs-${MY_PV}.tar.bz2"; LICENSE="GPL-2" SLOT="0" @@ -28,11 +28,6 @@ RDEPEND="${DEPEND} S="${WORKDIR}/wgs-${MY_PV}" -pkg_setup() { - python_set_active_version 2 - python_pkg_setup -} - src_prepare() { # epatch \ # "${FILESDIR}"/${P}-build.patch @@ -40,7 +35,7 @@ src_prepare() { } src_configure() { - cd "${S}/kmer" + cd "${S}/kmer" || die ./configure.sh || die } @@ -76,5 +71,5 @@ src_install() { dodoc README # avoid file collision - rm -f "${D}"/usr/bin/jellyfish + rm -f "${D}"/usr/bin/jellyfish || die }
