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# Copyright 1999-2015 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 /usr/bin/${x} ../share/${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
}
|
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