diff options
Diffstat (limited to 'sci-chemistry/cns/cns-1.3.ebuild')
| -rw-r--r-- | sci-chemistry/cns/cns-1.3.ebuild | 208 |
1 files changed, 208 insertions, 0 deletions
diff --git a/sci-chemistry/cns/cns-1.3.ebuild b/sci-chemistry/cns/cns-1.3.ebuild new file mode 100644 index 000000000000..22e5224782de --- /dev/null +++ b/sci-chemistry/cns/cns-1.3.ebuild @@ -0,0 +1,208 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.3.ebuild,v 1.1 2010/11/17 13:10:04 jlec Exp $ + +EAPI="3" + +inherit eutils fortran toolchain-funcs versionator flag-o-matic + +MY_PN="${PN}_solve" +MY_PV="$(delete_version_separator 2)" +MY_P="${MY_PN}_${MY_PV}" + +DESCRIPTION="Crystallography and NMR System" +HOMEPAGE="http://cns.csb.yale.edu/" +SRC_URI="${MY_P}_all.tar.gz + aria? ( aria2.3.1.tar.gz )" + +SLOT="0" +LICENSE="cns" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="aria openmp" + +RDEPEND="app-shells/tcsh" +DEPEND="${RDEPEND}" +PDEPEND="aria? ( ~sci-chemistry/aria-2.3.1 )" + +RESTRICT="fetch" +S="${WORKDIR}/${MY_P}" + +FORTRAN="gfortran ifc" + +pkg_nofetch() { + elog "Fill out the form at http://cns.csb.yale.edu/cns_request/" + use aria && elog "and http://aria.pasteur.fr/" + elog "and place these files:" + elog ${A} + elog "in ${DISTDIR}." +} + +pkg_setup() { + fortran_pkg_setup + + if [[ $(tc-getCC) == *gcc* ]] && + ( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] || + ! built_with_use sys-devel/gcc openmp ) + then + ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 " + ewarn "Switch CC to an OpenMP capable compiler" + fi +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-gentoo.patch \ + "${FILESDIR}"/${PV}-delete.patch + + if use aria; then + pushd "${WORKDIR}"/aria* >& /dev/null + # Update the cns sources in aria for version 1.2.1 + epatch "${FILESDIR}"/1.2.1-aria2.3.patch + + # Update the code with aria specific things + cp -rf cns/src/* "${S}"/source/ + popd >& /dev/null + fi + + # the code uses Intel-compiler-specific directives + if [[ ${FORTRANC} == gfortran ]]; then + use openmp && \ + OMPLIB="-lgomp" && append-flags -fopenmp + COMP="gfortran" + use amd64 && \ + append-fflags -fdefault-integer-8 + else + use openmp && OMPLIB="-liomp5" && \ + append-flags -openmp && append-ldflags -openmp + COMP="ifort" + use amd64 && append-fflags -i8 + append-fflags -Vaxlib + append-ldflags -Vaxlib + fi + + use amd64 && \ + append-cflags "-DINTEGER='long long int'" + + # Set up location for the build directory + # Uses obsolete `sort` syntax, so we set _POSIX2_VERSION + cp "${FILESDIR}"/cns_solve_env_sh-${PV} "${T}"/cns_solve_env_sh || die + sed -i \ + -e "s:_CNSsolve_location_:${S}:g" \ + -e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \ + "${S}"/cns_solve_env + sed -i \ + -e "s:_CNSsolve_location_:${S}:g" \ + -e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \ + "${T}"/cns_solve_env_sh + + ebegin "Fixing shebangs..." + find "${S}" -type f \ + -exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' \; || die + find . -name "Makefile*" \ + -exec \ + sed \ + -e "s:^SHELL=/bin/sh:SHELL=${EPREFIX}/bin/sh:g" \ + -e "s:/bin/ls:ls:g" \ + -e "s:/bin/rm:rm:g" \ + -i '{}' \; || die + eend +} + +src_compile() { + local GLOBALS + local MALIGN + + # Set up the compiler to use + pushd instlib/machine/unsupported/g77-unix 2>/dev/null + ln -s Makefile.header Makefile.header.${FORTRANC} || die + popd 2>/dev/null + + # make install really means build, since it's expected to be used in-place + # -j1 doesn't mean we do no respect MAKEOPTS! + emake -j1 \ + CC="$(tc-getCC)" \ + CXX="$(tc-getCXX)" \ + F77="${FORTRANC}" \ + LD="${FORTRANC}" \ + CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ + CXXFLAGS="${CXXFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ + LDFLAGS="${LDFLAGS}" \ + F77OPT="${FFLAGS:- -O2} ${MALIGN}" \ + F77STD="${GLOBALS}" \ + OMPLIB="${OMPLIB}" \ + compiler="${COMP}" \ + install \ + || die "emake failed" + +} + +src_test() { + # We need to force on g77 manually, because we can't get aliases working + # when we source in a -c + einfo "Running tests ..." + sh -c \ + "export CNS_G77=ON; source ${T}/cns_solve_env_sh; make run_tests" \ + || die "tests failed" + einfo "Displaying test results ..." + cat "${S}"/*_g77/test/*.diff-test +} + +src_install() { + cat >> "${T}"/66cns <<- EOF + CNS_SOLVE="${EPREFIX}/usr" + CNS_ROOT="${EPREFIX}/usr" + CNS_DATA="${EPREFIX}/usr/share/cns" + CNS_DOC="${EPREFIX}/usr/share/doc/cns-1.3" + CNS_LIB="${EPREFIX}/usr/share/cns/libraries" + CNS_MODULE="${EPREFIX}/usr/share/cns/modules" + CNS_TOPPAR="${EPREFIX}/usr/share/cns/libraries/toppar" + CNS_CONFDB="${EPREFIX}/usr/share/cns/libraries/confdb" + CNS_XTALLIB="${EPREFIX}/usr/share/cns/libraries/xtal" + CNS_NMRLIB="${EPREFIX}/usr/share/cns/libraries/nmr" + CNS_XRAYLIB="${EPREFIX}/usr/share/cns/libraries/xray" + CNS_XTALMODULE="${EPREFIX}/usr/share/cns/modules/xtal" + CNS_NMRMODULE="${EPREFIX}/usr/share/cns/modules/nmr" + CNS_HELPLIB="${EPREFIX}/usr/share/cns/helplib" + EOF + + doenvd "${T}"/66cns || die + + # Don't want to install this + rm -f "${S}"/*linux*/utils/Makefile + + sed -i \ + -e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \ + "${S}"/bin/cns_web || die + + newbin "${S}"/*linux*/bin/cns_solve* cns_solve \ + || die "install cns_solve failed" + + # Can be run by either cns_solve or cns + dosym cns_solve /usr/bin/cns + + dobin \ + "${S}"/*linux*/utils/* \ + "${S}"/bin/cns_{edit,header,import_cif,transfer,web} || die "install bin failed" + + insinto /usr/share/cns + doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib "${S}"/bin/cns_info || die + + dohtml \ + -A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \ + -f all_cns_info_template,omac,def \ + -r doc/html/* || die + # Conflits with app-text/dos2unix + rm -f "${D}"/usr/bin/dos2unix || die +} + +pkg_info() { + if use openmp; then + elog "Set OMP_NUM_THREADS to the number of threads you want." + elog "If you get segfaults on large structures, set the GOMP_STACKSIZE" + elog "variable if using gcc (16384 should be good)." + fi +} + +pkg_postinst() { + pkg_info +} |