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Diffstat (limited to 'sci-chemistry/ambertools/ambertools-1.5-r4.ebuild')
| -rw-r--r-- | sci-chemistry/ambertools/ambertools-1.5-r4.ebuild | 159 |
1 files changed, 159 insertions, 0 deletions
diff --git a/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild new file mode 100644 index 000000000..d689579f9 --- /dev/null +++ b/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild @@ -0,0 +1,159 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild,v 1.2 2011/08/02 14:42:37 alexxy Exp $ + +EAPI=4 + +inherit eutils fortran-2 toolchain-funcs + +DESCRIPTION="A suite for carrying out complete molecular mechanics investigations" +HOMEPAGE="http://ambermd.org/#AmberTools" +SRC_URI=" + AmberTools-${PV}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="openmp X" + +RESTRICT="fetch" + +RDEPEND=" + virtual/cblas + virtual/lapack + sci-libs/clapack + sci-libs/arpack + sci-libs/cifparse-obj + sci-chemistry/mopac7 + sci-libs/netcdf + sci-libs/fftw:2.1 + sci-chemistry/reduce + virtual/fortran" +DEPEND="${RDEPEND} + dev-util/byacc + dev-libs/libf2c + sys-devel/ucpp" +S="${WORKDIR}/amber11" + +pkg_nofetch() { + einfo "Go to ${HOMEPAGE} and get ${A}" + einfo "Place it in ${DISTDIR}" +} + +pkg_setup() { + fortran-2_pkg_setup + if use openmp; then + tc-has-openmp || \ + die "Please select an openmp capable compiler like gcc[openmp]" + fi + AMBERHOME="${S}" +} + +src_prepare() { + epatch \ + "${FILESDIR}/${P}-bugfix_1-21.patch" \ + "${FILESDIR}/${P}-bugfix_22-27.patch" \ + "${FILESDIR}/${P}-bugfix_28.patch" \ + "${FILESDIR}/${P}-gentoo2.patch" \ + "${FILESDIR}/${P}-overflow.patch" + cd "${S}"/AmberTools/src + rm -r \ + arpack \ + blas \ + byacc \ + lapack \ + fftw-2.1.5 \ + fftw-3.2.2 \ + c9x-complex \ + cifparse \ + netcdf \ + pnetcdf \ + reduce \ + ucpp-1.3 \ + || die +} + +src_configure() { + cd "${S}"/AmberTools/src + sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \ + -e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \ + -e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \ + -e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ + -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a: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:fc=g77:fc=$(tc-getFC):g" \ + -e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \ + -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \ + -i configure || die + sed -e "s:arsecond_:arscnd_:g" \ + -i sff/time.c \ + -i sff/sff.h \ + -i sff/sff.c || die + sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \ + -i nss/Makefile || die + + local myconf + + use X || myconf="${myconf} -noX11" + + use openmp && myconf="${myconf} -openmp" + + ./configure \ + ${myconf} \ + -nobintraj \ + -nomdgx \ + -nomtkpp \ + -nopython \ + -nosleap \ + gnu +} + +src_compile() { + cd "${S}"/AmberTools/src + emake || die +} + +src_test() { + cd "${S}"/AmberTools/test + make test || die +} + +src_install() { + rm -r bin/chemistry bin/MMPBSA_mods + rm bin/ante-MMPBSA.py bin/extractFrcmod.py + + for x in bin/* + do dobin ${x} || die + done + + dobin AmberTools/src/antechamber/mopac.sh + sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \ + -i "${ED}/usr/bin/mopac.sh" || die + + # Make symlinks untill binpath for amber will be fixed + dodir /usr/share/${PN}/bin + cd "${ED}/usr/bin" + for x in * + do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x} + done + cd "${S}" + + dodoc doc/AmberTools.pdf doc/leap_pg.pdf + dolib.a lib/* + insinto /usr/include/${PN} + doins include/* + insinto /usr/share/${PN} + doins -r dat + cd AmberTools + doins -r benchmarks + doins -r examples + doins -r test + + cat >> "${T}"/99ambertools <<- EOF + AMBERHOME="${EPREFIX}/usr/share/ambertools" + EOF + doenvd "${T}"/99ambertools +} |