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

(Portage version: 2.1.10.44/git/Linux i686, unsigned Manifest commit)

4 files changed, 92 insertions, 0 deletions

diff --git a/sci-biology/wgs-assembler/ChangeLog b/sci-biology/wgs-assembler/ChangeLog
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+++ b/sci-biology/wgs-assembler/ChangeLog
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+# 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/Manifest b/sci-biology/wgs-assembler/Manifest
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index 000000000..dc9eb4bc9
--- /dev/null
+++ b/sci-biology/wgs-assembler/Manifest
@@ -0,0 +1 @@
+DIST wgs-7.0.tar.bz2 1952253 SHA256 fee425cf2ec6aec6e98d580cc7e43b53eb37abd7ca14e3edc1f953d2c09b3a6c SHA512 e5ef1d4533e3dd17d13c6aca9631f5300768a258f8241f3f7f90de3785bf7a340b6896febe335682c282434c9983bc4a02fe2128a5b0e7ec415dd65e0fe400ba WHIRLPOOL a158b882e51e8ff80fa4e6bcbe4322125fce65fc64900407882a728de9465b778f59cc6d543142ca65a255295e66e89e5303774eeef7a66362c5f492ae99a92b
diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml
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+++ b/sci-biology/wgs-assembler/metadata.xml
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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild
new file mode 100644
index 000000000..b75a5b79a
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild
@@ -0,0 +1,70 @@
+# 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
+}