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diff --git a/sci-chemistry/theseus/theseus-3.0.0.ebuild b/sci-chemistry/theseus/theseus-3.0.0.ebuild
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+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit multilib toolchain-funcs
+
+DESCRIPTION="Maximum likelihood superpositioning and analysis of macromolecular structures"
+HOMEPAGE="http://www.theseus3d.org/"
+SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RDEPEND="
+	sci-libs/gsl
+	|| (
+		sci-biology/muscle
+		sci-biology/probcons
+		sci-biology/mafft
+		sci-biology/t-coffee
+		sci-biology/kalign
+		sci-biology/clustalw:2
+		)"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}"/${PN}_src/
+
+src_prepare() {
+	cat >> make.inc <<- EOF
+	ARCH = $(tc-getAR)
+	ARCHFLAGS = -rvs
+	RANLIB = $(tc-getRANLIB)
+	LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir)
+	SYSLIBS = $(pkg-config --libs gsl) -lpthread
+	LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
+	LIBDIR = -L./lib
+	INSTALLDIR = "${ED}"/usr/bin
+	OPT =
+	WARN =
+	CFLAGS = ${CFLAGS} -std=c11 \$(WARN)
+	CC = $(tc-getCC)
+	EOF
+
+	sed \
+		-e 's|theseus:|theseus: libs|g' \
+		-e '/-o theseus/s:$(CC):$(CC) ${LDFLAGS}:g' \
+		-i Makefile || die
+
+	sed \
+		-e 's:/usr/bin/sed:sed:g' \
+		-e "s:/usr/local/bin/:/usr/bin/:g" \
+		-e "s:/usr/bin/:${EPREFIX}/usr/bin/:g" \
+		-i theseus_align || die
+}
+
+src_compile () {
+	emake ltheseus
+	default
+}
+
+src_install() {
+	dobin theseus theseus_align
+	dodoc theseus_man.pdf README AUTHORS
+	use examples && insinto /usr/share/${PN} && doins -r examples
+}