[gentoo-commits] proj/sci:master commit in: sci-biology/wgs-assembler/

[Justin Lecher]

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
 }