diff options
Diffstat (limited to 'sci-chemistry/ccp4/ccp4-6.0.1.ebuild')
| -rw-r--r-- | sci-chemistry/ccp4/ccp4-6.0.1.ebuild | 432 |
1 files changed, 0 insertions, 432 deletions
diff --git a/sci-chemistry/ccp4/ccp4-6.0.1.ebuild b/sci-chemistry/ccp4/ccp4-6.0.1.ebuild deleted file mode 100644 index d3a1e56b5431..000000000000 --- a/sci-chemistry/ccp4/ccp4-6.0.1.ebuild +++ /dev/null @@ -1,432 +0,0 @@ -# Copyright 1999-2006 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ccp4-6.0.1.ebuild,v 1.1 2006/06/16 20:46:02 spyderous Exp $ - -inherit fortran eutils gnuconfig toolchain-funcs - -FORTRAN="g77 gfortran ifc" - -SRC="ftp://ftp.ccp4.ac.uk/ccp4" - -PATCH_TOT="0" -#PATCH1=( src -# anisoanl.f-r1.22-r1.24.diff ) -#PATCH2=( src/sc_ -# sc.f-r1.9-r1.9.2.1.diff ) -#PATCH3=( src/sc_ -# setup.fh-r1.5-r1.5.2.1.diff ) - -DESCRIPTION="Protein X-ray crystallography toolkit" -HOMEPAGE="http://www.ccp4.ac.uk/" -RESTRICT="mirror stricter" -SRC_URI="${SRC}/${PV}/packed/${P}-core-src.tar.gz" -# ${SRC}/${PV}/patches/${PATCH1[1]} -# ${SRC}/${PV}/patches/${PATCH2[1]} -# ${SRC}/${PV}/patches/${PATCH3[1]}" -LICENSE="ccp4" -SLOT="0" -KEYWORDS="~ppc ~x86" -IUSE="X" -# app-office/sc overlaps sc binary and man page -# We can't rename ours since the automated ccp4i interface expects it there, -# as do many scripts. app-office/sc can't rename its because that's the name -# of the package. -RDEPEND="X? ( - || ( - ( - x11-libs/libX11 - x11-libs/libXt - x11-libs/libXaw - ) - virtual/x11 - ) - ) - >=dev-lang/tcl-8.3 - >=dev-lang/tk-8.3 - >=dev-tcltk/blt-2.4 - virtual/lapack - virtual/blas - =sci-libs/fftw-2* - sci-chemistry/pdb-extract - sci-chemistry/rasmol - sci-libs/mccp4 - || ( app-shells/tcsh app-shells/csh ) - !app-office/sc" -# >=sys-apps/portage-2.1.1_pre1 for RESTRICT=stricter -# Otherwise portage dies instead of fixing RPATHs -DEPEND="${RDEPEND} - X? ( - || ( - ( - x11-misc/imake - x11-proto/inputproto - x11-proto/xextproto - ) - virtual/x11 - ) - ) - >=sys-apps/portage-2.1.1_pre1" - -S="${WORKDIR}/${PN}-${PV}" - -src_unpack() { - unpack ${A} - cd ${S} - - einfo "Applying upstream patches ..." - for patch in $(seq $PATCH_TOT); do - base="PATCH${patch}" - dir=$(eval echo \${${base}[0]}) - p=$(eval echo \${${base}[1]}) - pushd ${dir} >& /dev/null - ccp_patch ${DISTDIR}/${p} - popd >& /dev/null - done - einfo "Done." - echo - - einfo "Applying Gentoo patches ..." - # These two only needed when attempting to install outside build dir via - # --bindir and --libdir instead of straight copying after build - - # it attempts to install some libraries during the build - #ccp_patch ${FILESDIR}/${P}-install-libs-at-install-time.patch - # hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view - # without this patch when --libdir is set - # Rotgen still needs more patching to find it - #ccp_patch ${FILESDIR}/add-xdl-libdir.patch - - # it tries to create libdir, bindir etc on live system in configure - ccp_patch ${FILESDIR}/${PV}-dont-make-dirs-in-configure.patch - - # We already have sci-chemistry/rasmol - ccp_patch ${FILESDIR}/dont-build-rasmol.patch - - # We already have sci-chemistry/pdb-extract -# Use configure option instead -# ccp_patch ${FILESDIR}/dont-build-pdb-extract.patch - - ccp_patch ${FILESDIR}/create-mosflm-bindir.patch - ccp_patch ${FILESDIR}/make-mosflm-libdir.patch - ccp_patch ${FILESDIR}/make-mosflm-index-libdir.patch - ccp_patch ${FILESDIR}/make-mosflm-cbf-libdir.patch - ccp_patch ${FILESDIR}/make-ipmosflm-dir.patch - -# Don't use these when we aren't building phaser -# ccp_patch ${FILESDIR}/make-phaser-bindir.patch -# ccp_patch ${FILESDIR}/no-phaser-ld-assume-kernel.patch -# # scons config.py tries to chmod python on live system -# ccp_patch ${FILESDIR}/dont-chmod-python-binary.patch - - # Don't use this when we aren't building clipper - # For some reason clipper check for $enableval even when --enable is passed - ccp_patch ${FILESDIR}/pass-clipper-enablevals.patch - ccp_patch ${FILESDIR}/clipper-find-mccp4-includes.patch - - # Default to firefox browser, not 'netscape' - ccp_patch ${FILESDIR}/ccp4i-default-to-firefox.patch - - # Also use -lpthread when linking blas and lapack - # We may need more fixing to use libcblas for the C files - ccp_patch ${FILESDIR}/check-blas-lapack-pthread.patch - - # gerror_ gets defined twice on ppc if you're using gfortran/g95 - ccp_patch ${FILESDIR}/${PV}-ppc-double-define-gerror.patch - - einfo "Done." # done applying Gentoo patches - echo - - gnuconfig_update -} - -src_compile() { - # GENTOO_OSNAME can be one of: - # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd - # linux_compaq_compilers linux_intel_compilers generic Darwin - # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers - if [[ "${FORTRANC}" = "ifc" ]]; then - if use ia64; then - GENTOO_OSNAME="ia64_linux_intel" - else - # Should be valid for x86, maybe amd64 - GENTOO_OSNAME="linux_intel_compilers" - fi - else - # Should be valid for x86 and amd64, at least - GENTOO_OSNAME="linux" - fi - - # Sets up env - ln -s \ - ccp4.setup-bash \ - ${S}/include/ccp4.setup - - # We agree to the license by emerging this, set in LICENSE - sed -i \ - -e "s~^\(^agreed=\).*~\1yes~g" \ - ${S}/configure - - # Fix up variables -- need to reset CCP4_MASTER at install-time - sed -i \ - -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ - -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \ - ${S}/include/ccp4.setup* - - # Set up variables for build - source ${S}/include/ccp4.setup - - export CC=$(tc-getCC) - export CXX=$(tc-getCXX) - export COPTIM=${CFLAGS} - export CXXOPTIM=${CXXFLAGS} - # Default to -O2 if FFLAGS is unset - export FC=${FORTRANC} - export FOPTIM=${FFLAGS:- -O2} - - # Add xdl libraries to library search path - # Note: some of configure attaches CCP4_LIB to -L, and other parts - # append libfoo.a immediately after it, so it can only be a single path. - export CCP4_LIB="${CCP4}/x-windows/xdl_view/src/.libs" - - # Can't use econf, configure rejects unknown options like --prefix - ./configure \ - $(use_enable X x) \ - --with-shared-libs \ - --with-fftw=/usr \ - --with-warnings \ - --disable-pdb_extract \ - --disable-cctbx \ - --disable-phaser \ - --tmpdir="${TMPDIR}" \ - ${GENTOO_OSNAME} || die "econf failed" - emake -j1 || die "emake failed" -} - -src_install() { -# Only needed when using --bindir and --libdir - # Needed to avoid errors. Originally tried to make lib and bin - # in configure script, now patched out by dont-make-dirs-in-configure.patch -# dodir /usr/include /usr/$(get_libdir) /usr/bin - -# make install || die "install failed" - einstall || die "install failed" - - # Fix env - sed -i \ - -e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \ - -e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \ - -e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \ - -e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \ - -e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \ - -e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \ - -e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \ - -e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \ - ${S}/include/ccp4.setup* - - # Get rid of S instances - # Also the main clipper library is built as libclipper-core, not libclipper - sed -i \ - -e "s:${S}:${ROOT}usr:g" \ - -e "s:lclipper :lclipper-core :g" \ - ${S}/bin/clipper-config -# sed -i \ -# -e "s:${S}:${ROOT}usr:g" \ -# ${S}/$(get_libdir)/cctbx/cctbx_build/setpaths* - - # Bins - EXEDESTTREE="/usr/bin" doexe ${S}/bin/* - - # Libs - for file in ${S}/lib/*; do - if [[ -d ${file} ]]; then - continue - elif [[ -x ${file} ]]; then - dolib.so ${file} - else - INSDESTTREE="/usr/$(get_libdir)" doins ${file} - fi - done - - # Fix libdir in all *.la files - sed -i \ - -e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \ - ${D}/usr/$(get_libdir)/*.la - - # Library symlinks - local LIBNAMES="libclipper-ccp4.so.0.0.0 - libclipper-cif.so.0.0.0 - libclipper-contrib.so.0.0.0 - libclipper-core.so.0.0.0 - libclipper-minimol.so.0.0.0 - libclipper-mmdbold.so.0.0.0 - libclipper-mmdb.so.0.0.0 - libclipper-mtz.so.1.0.0 - libclipper-phs.so.0.0.0 - libjwc_c.so.0.1.1 - libjwc_f.so.0.1.1 - libssm.so.0.0.0 - libxdl_viewextra.so.0.0.0 - libxdl_view.so.2.0.0" - - for LIBNAME in ${LIBNAMES}; do - library_dosym ${LIBNAME} - done - -# dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so -# dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0 -# dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0.0 -# -# dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so -# dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0 -# dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0.0 -# -# dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so -# dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0 -# dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0.0 -# -# dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so -# dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0 -# dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0.0 -# -# dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so -# dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0 -# dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0.0 -# -# dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so -# dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0 -# dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0.0 -# -# dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so -# dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0 -# dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0.0 -# -# dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so -# dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1 -# dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1.0 -# -# dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so -# dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0 -# dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0.0 -# -# dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so -# dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0 -# dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0.1 -# -# dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so -# dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0 -# dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0.1 -# -# dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so -# dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0 -# dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0.0 -# -# dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so -# dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0 -# dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0.0 -# -# dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so -# dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2 -# dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2.0 - - # Environment files, setup scripts, etc. - INSDESTTREE="/usr/share/ccp4/include" doins ${S}/include/* - - # CCP4Interface - GUI - INSDESTTREE="/usr/$(get_libdir)/ccp4" doins -r ${S}/ccp4i - EXEDESTTREE="/usr/$(get_libdir)/ccp4/ccp4i/bin" doexe ${S}/ccp4i/bin/* - - # Data - INSDESTTREE="/usr/share/ccp4" doins -r ${S}/lib/data - - # Include files - for i in ccp4 clipper mmdb ssm; do - INSDESTTREE="/usr/include" doins -r ${S}/include/${i} - done - - # Install docs and examples - - doman ${S}/man/cat1/* - - mv ${S}/manual/README ${S}/manual/README-manual - dodoc ${S}/manual/* - - dodoc ${S}/README ${S}/CHANGES - - dodoc ${S}/doc/* - rm ${D}/usr/share/doc/${PF}/GNUmakefile.gz - rm ${D}/usr/share/doc/${PF}/COPYING.gz - - dohtml -r ${S}/html/* - dodoc ${S}/examples/README - - # Fix wrongly installed HTML pages from clipper - dohtml "${D}"/usr/html/* - rm -rf "${D}"/usr/html - - for i in data rnase toxd; do - DOCDESTTREE="examples/${i}" dodoc ${S}/examples/${i}/* - done - - DOCDESTTREE="examples/tutorial" dohtml -r ${S}/examples/tutorial/html - DOCDESTTREE="examples/tutorial" dohtml examples/tutorial/tut.css - for i in data results; do - DOCDESTTREE="examples/tutorial/${i}" dodoc ${S}/examples/tutorial/${i}/* - done - - for i in non-runnable runnable; do - DOCDESTTREE="examples/unix/${i}" dodoc ${S}/examples/unix/${i} - done - - # Needed for ccp4i docs to work - dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples - dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html - - # Fix overlaps with other packages - rm ${D}/usr/share/man/man1/rasmol.1.gz -} - -pkg_postinst() { - einfo "The Web browser defaults to firefox. Change CCP4_BROWSER" - einfo "in /usr/share/ccp4/include/ccp4.setup* to modify this." - - ewarn "Set your .bashrc or other shell login file to source" - ewarn "one of the ccp4.setup* files in ${ROOT}usr/share/ccp4/include." - ewarn "CCP4 will not work without this." -} - -# Epatch wrapper for bulk patching -ccp_patch() { - EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} -} - -# Links libname.so, libname.so.major and libname.so.major.minor -# to libname.so.major.minor.micro -library_dosym() { - local LIBNAME LIBDIR SUFFIX CORE_LIBNAME LIB_MAJOR LIB_MINOR LIB_VERSIONS - - LIBNAME=${1} - LIBDIR=${2:-/usr/$(get_libdir)} - - # Tag / on the end of libdir if needed - if [[ ${LIBDIR:$((${#LIBDIR}-1)):1} != "/" ]]; then - LIBDIR="${LIBDIR}/" - fi - - if [[ "${LIBNAME}" != *.so.* ]]; then - msg="library_dosym() requires a shared, versioned library as an argument" - eerror "$msg" - die "$msg" - fi - - SUFFIX=${LIBNAME##*so.} - CORE_LIBNAME=${LIBNAME%.so.*} - CORE_LIBNAME="${CORE_LIBNAME}.so" - LIB_MAJOR=${SUFFIX%%.*} - LIB_MINOR=${SUFFIX#*.} - LIB_MINOR=${SUFFIX%%.*} - LIB_VERSIONS="${LIB_MAJOR} ${LIB_MAJOR}.${LIB_MINOR}" - for LIB_SUFFIX in .${LIB_MAJOR} .${LIB_MAJOR}.${LIB_MINOR} ""; do - einfo "Calling dosym ${LIBNAME} ${LIBDIR} ${CORE_LIBNAME} ${LIB_SUFFIX}" - dosym ${LIBNAME} ${LIBDIR}${CORE_LIBNAME}${LIB_SUFFIX} - done -} |