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Diffstat (limited to 'sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild')
-rw-r--r--sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild75
1 files changed, 75 insertions, 0 deletions
diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild
new file mode 100644
index 000000000000..b3ac7c30813b
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild
@@ -0,0 +1,75 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+PYTHON_DEPEND=2
+
+inherit eutils python 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"
+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
+}