1 files changed, 165 insertions, 0 deletions
diff --git a/sci-chemistry/ambertools/ambertools-12_p38-r1.ebuild b/sci-chemistry/ambertools/ambertools-12_p38-r1.ebuild
new file mode 100644
index 000000000..e6beea259
--- /dev/null
+++ b/sci-chemistry/ambertools/ambertools-12_p38-r1.ebuild
@@ -0,0 +1,165 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils fortran-2 multilib multiprocessing toolchain-funcs
+
+DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
+HOMEPAGE="http://ambermd.org/#AmberTools"
+SRC_URI="
+	AmberTools${PV%_p*}.tar.bz2
+	http://dev.gentoo.org/~jlec/distfiles/${PN}-bugfixes-${PV}.tar.xz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE="openmp X"
+
+RESTRICT="fetch"
+
+RDEPEND="
+	virtual/cblas
+	virtual/lapack
+	sci-libs/clapack
+	sci-libs/arpack
+	sci-libs/cifparse-obj
+	sci-chemistry/mopac7
+	sci-libs/netcdf
+	>=sci-libs/fftw-3.3:3.0
+	sci-chemistry/reduce"
+DEPEND="${RDEPEND}
+	app-shells/tcsh
+	dev-util/byacc
+	dev-libs/libf2c
+	sys-devel/ucpp"
+
+S="${WORKDIR}/amber12"
+
+pkg_nofetch() {
+	einfo "Go to ${HOMEPAGE} and get AmberTools${PV%_p*}.tar.bz2"
+	einfo "and download http://dev.gentoo.org/~jlec/distfiles/${PN}-bugfixes-${PV}.tar.xz"
+	einfo "Place both into ${DISTDIR}"
+}
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	if use openmp; then
+		tc-has-openmp || \
+			die "Please select an openmp capable compiler like gcc[openmp]"
+	fi
+	export AMBERHOME="${S}"
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-gcc5.patch \
+		"${FILESDIR}"/${P}-format-security.patch \
+		"${FILESDIR}"/${PN}-12-gentoo.patch \
+		"${WORKDIR}"/bugfixes/bugfix.{14..38}
+	cd "${S}"/AmberTools/src || die
+	rm -r \
+		arpack \
+		blas \
+		byacc \
+		lapack \
+		fftw-3.3 \
+		c9x-complex \
+		cifparse \
+		netcdf \
+		reduce \
+		ucpp-1.3 \
+		|| die
+
+	cd "${S}"/AmberTools/src || die
+	sed \
+		-e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
+		-e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
+		-e "s:-llapack:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
+		-e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
+		-e "s:-lblas:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
+		-e "s:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \
+		-e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \
+		-e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
+		-e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \
+		-e "s:GENTOO_INCLUDE:${EPREFIX}/usr/include:g" \
+		-e "s:GENTOO_FFTW3_LIBS:$($(tc-getPKG_CONFIG) fftw3 --libs):" \
+		-e "s:fc=g77:fc=$(tc-getFC):g" \
+		-e "s:\$netcdfflag:$($(tc-getPKG_CONFIG) netcdf --libs):g" \
+		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
+		-i configure2 || die
+
+	sed \
+		-e "s:arsecond_:arscnd_:g" \
+		-i sff/time.c sff/sff.h sff/sff.c || die
+
+}
+
+src_configure() {
+	local myconf="--no-updates"
+
+	use X || myconf="${myconf} -noX11"
+
+	use openmp && myconf="${myconf} -openmp"
+
+	cd "${S}" || die
+
+	sed \
+		-e '/patch_amber.py/d' \
+		-i configure || die
+
+	./configure \
+		${myconf} \
+		-nobintraj \
+		-nomtkpp \
+		gnu || die
+}
+
+src_test() {
+	use openmp && export OMP_NUM_THREADS=$(makeopts_jobs)
+
+	emake test
+}
+
+src_compile() {
+	emake \
+		CC=$(tc-getCC) \
+		FC=$(tc-getFC)
+}
+
+src_install() {
+	rm bin/*.py || die
+
+	for x in bin/*
+	do
+		[ ! -d ${x} ] && dobin ${x}
+	done
+
+	dobin AmberTools/src/antechamber/mopac.sh
+	sed \
+		-e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
+		-i "${ED}/usr/bin/mopac.sh" || die
+
+	# Make symlinks untill binpath for amber will be fixed
+	dodir /usr/share/${PN}/bin
+	cd "${ED}/usr/bin" || die
+	for x in *; do
+		dosym ../../../bin/${x} /usr/share/${PN}/bin/${x}
+	done
+	cd "${S}" || die
+
+	dodoc doc/AmberTools12.pdf
+	dolib.a lib/*
+	insinto /usr/include/${PN}
+	doins include/*
+	insinto /usr/share/${PN}
+	doins -r dat
+	cd AmberTools || die
+	doins -r benchmarks examples test
+
+	cat >> "${T}"/99ambertools <<- EOF
+	AMBERHOME="${EPREFIX}/usr/share/ambertools"
+	EOF
+	doenvd "${T}"/99ambertools
+}