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diff --git a/sci-biology/mummer/mummer-3.22-r1.ebuild b/sci-biology/mummer/mummer-3.22-r1.ebuild
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+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="3"
+
+inherit eutils flag-o-matic
+
+DESCRIPTION="A rapid whole genome aligner"
+HOMEPAGE="http://mummer.sourceforge.net/"
+SRC_URI="mirror://sourceforge/mummer/MUMmer${PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE="doc"
+KEYWORDS="amd64 x86"
+
+DEPEND=""
+RDEPEND="app-shells/tcsh"
+
+S="${WORKDIR}/MUMmer${PV}"
+
+src_prepare() {
+	use amd64 && append-flags -DSIXTYFOURBITS
+
+	epatch \
+		"${FILESDIR}"/${PV}-prll.patch \
+		"${FILESDIR}"/${PV}-ldflags.patch
+
+	sed \
+		-e '/^CFLAGS/d' \
+		-e '/^CXXFLAGS/d' \
+		-e '/^LDFLAGS/d' \
+		-i Makefile || die
+}
+
+src_compile() {
+	emake || die
+
+	sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \
+		-e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \
+		-e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \
+		-e 's|\(set bindir = \).*|\1/usr/bin|' \
+		-e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \
+		-e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \
+		scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die
+	mv annotate mummer-annotate || die
+	sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh || die
+}
+
+src_install() {
+	dobin $(find . -maxdepth 1 -type f -executable) aux_bin/* || die
+
+	insinto /usr/share/${PN}/scripts
+	doins scripts/{*.awk,*.csh,*.pl} || die
+	insinto /usr/share/${PN}/lib
+	doins scripts/Foundation.pm || die
+
+	dodoc ACKNOWLEDGEMENTS ChangeLog README || die
+	insinto /usr/share/doc/${PF}
+	if use doc; then
+		doins -r docs || die
+	fi
+}