--- /dev/null
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r3.ebuild,v 1.1 2010/05/22 11:34:22 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+
+inherit autotools eutils flag-o-matic fortran gnuconfig python toolchain-funcs
+
+FORTRAN="g77 gfortran ifc"
+
+MY_P="${PN/-apps}-${PV}"
+
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
+
+#UPDATE="04_03_09"
+#PATCHDATE="090511"
+
+PATCH_TOT="0"
+# Here's a little scriptlet to generate this list from the provided
+# index.patches file
+#
+# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
+# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
+# index.patches
+#PATCH1=( src/topp_
+#topp.f-r1.16.2.5-r1.16.2.6.diff )
+#PATCH2=( .
+#configure-r1.372.2.18-r1.372.2.19.diff )
+
+DESCRIPTION="Protein X-ray crystallography toolkit"
+HOMEPAGE="http://www.ccp4.ac.uk/"
+RESTRICT="mirror"
+SRC_URI="
+ ${SRC}/${PV}/${MY_P}-core-src.tar.gz
+ http://dev.gentooexperimental.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2"
+# patch tarball from upstream
+ [[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
+# patches created by us
+ [[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
+
+for i in $(seq $PATCH_TOT); do
+ NAME="PATCH${i}[1]"
+ SRC_URI="${SRC_URI}
+ ${SRC}/${PV}/patches/${!NAME}"
+done
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="examples X"
+
+X11DEPS="
+ x11-libs/libX11
+ x11-libs/libXaw
+ x11-libs/libXt
+ x11-libs/libjwc_c
+ x11-libs/libjwc_f
+ x11-libs/libxdl_view"
+
+TKDEPS="
+ >=dev-lang/tk-8.3
+ >=dev-tcltk/blt-2.4
+ dev-tcltk/iwidgets
+ dev-tcltk/itcl
+ dev-tcltk/itk
+ >=dev-tcltk/tdom-0.8
+ dev-tcltk/tkimg
+ dev-tcltk/tktreectrl"
+
+SCILIBS="
+ ~sci-libs/ccp4-libs-${PV}
+ !<=sci-libs/ccp4-libs-${PV}-r2
+ sci-libs/clipper
+ =sci-libs/fftw-2*
+ sci-libs/mmdb
+ virtual/blas
+ virtual/lapack"
+
+SCIAPPS="
+ sci-chemistry/pdb-extract
+ sci-chemistry/pymol
+ sci-chemistry/rasmol
+ >=sci-chemistry/oasis-4.0-r1"
+
+RDEPEND="
+ ${TKDEPS}
+ ${SCILIBS}
+ app-shells/tcsh
+ dev-python/pyxml
+ dev-libs/libxml2
+ dev-libs/boehm-gc
+ !app-office/sc
+ !<sci-chemistry/ccp4-6.1.2
+ X? ( ${X11DEPS} )"
+DEPEND="${RDEPEND}
+ =sys-devel/automake-1.6*
+ X? (
+ x11-misc/imake
+ x11-proto/inputproto
+ x11-proto/xextproto
+ )"
+PDEPEND="${SCIAPPS}"
+
+S="${WORKDIR}/${MY_P}"
+
+pkg_setup() {
+ python_set_active_version 2
+ fortran_pkg_setup
+}
+
+src_prepare() {
+ 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
+
+ [[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
+
+ einfo "Applying Gentoo patches ..."
+
+ # 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
+ # Also remember to create the bindir.
+ ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch
+
+ # libraries come from sci-libs/ccp4-libs
+ ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch
+
+ # coreutils installs a binary called truncate
+# ccp_patch "${FILESDIR}"/${PV}-rename-truncate.patch
+# mv ./doc/truncate.doc ./doc/ftruncate.doc || die
+# mv ./html/truncate.html ./html/ftruncate.html || die
+
+ # conflicts with media-libs/raptor
+# ccp_patch "${FILESDIR}"/${PV}-rename-rapper.patch
+# mv ./doc/rapper.doc ./doc/rappermc.doc || die
+# mv ./html/rapper.html ./html/rappermc.html || die
+
+ # We have seperate ebuilds for those
+ for bin in molref xia scala imosflm balbes; do
+ ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch
+ done
+
+ # don't configure what is not build
+ ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch
+
+ # Set python paths correctly
+ ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch
+
+ # Set python paths correctly
+ ccp_patch "${FILESDIR}"/${PV}-pisa.patch
+
+ # Set python paths correctly
+ ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch
+
+ # Update things for oasis 4 usage
+ epatch "${WORKDIR}"/${PV}-oasis4.0.patch
+ sed 's: oasis : :g' -i src/Makefile.in || die
+
+ einfo "Done." # done applying Gentoo patches
+ echo
+
+ # Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version
+ sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure
+
+ # Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
+ pushd src/rapper 2>/dev/null
+ sed -i \
+ -e '/^AC_CONFIG_SUBDIRS(\[gc7.0 libxml2\])/d' \
+ configure.ac
+ sed -i \
+ -e '/^SUBDIRS/s:libxml2 gc7.0::g' \
+ Makefile.am
+ sed -i \
+ -e '/^rappermc_LDADD/s:../gc7.0/libgc.la ../libxml2/libxml2.la:-lgc -lxml2:g' \
+ LOOP/Makefile.am
+ sed -i \
+ -e '/^INCLUDES/s:-I../gc7.0/include -I../libxml2/include:-I${EPREFIX}/usr/include/gc -I${EPREFIX}/usr/include/libxml2:g' \
+ LOOP/Makefile.am
+ eautoreconf
+ popd 2>/dev/null
+
+ gnuconfig_update
+
+ python_convert_shebangs $(python_get_version) src/ccp4_pipeline_simple.py ./share/smartie/*.py
+}
+
+src_configure() {
+ # Build system is broken if we set LDFLAGS
+ unset LDFLAGS
+
+ # These are broken with ./src/procheck/ps.f
+ filter-flags "-floop-*"
+
+ # GENTOO_OSNAME can be one of:
+ # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
+ # linux_compaq_compilers linux_intel_compilers generic Darwin
+ # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
+ if [[ "${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~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
+ -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
+ -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
+ -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
+ -e "s~^\(export CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
+ "${S}"/include/ccp4.setup*
+
+ # Set up variables for build
+ source "${S}"/include/ccp4.setup-sh
+
+ export CC=$(tc-getCC)
+ export CXX=$(tc-getCXX)
+ export COPTIM=${CFLAGS}
+ export CXXOPTIM=${CXXFLAGS}
+ # Default to -O2 if FFLAGS is unset
+ export FC=${FORTRANC}
+ export FOPTIM=${FFLAGS:- -O2}
+ export BINSORT_SCR="${T}"
+ export CCP4_MASTER="${WORKDIR}"
+ export CCP4I_TCLTK="${EPREFIX}/usr/bin"
+
+ # Can't use econf, configure rejects unknown options like --prefix
+ ./configure \
+ $(use_enable X x) \
+ --with-shared-libs \
+ --with-fftw="${EPREFIX}"/usr \
+ --with-warnings \
+ --disable-pdb_extract \
+ --disable-cctbx \
+ --disable-phaser \
+ --disable-diffractionImg \
+ --disable-clipper \
+ --disable-mosflm \
+ --disable-mrbump \
+ --tmpdir="${TMPDIR}" \
+ ${GENTOO_OSNAME} || die "econf failed"
+
+ # We do this manually, since disabling the clipper libraries also
+ # disables the clipper programs
+ pushd src/clipper_progs 2>/dev/null
+ econf \
+ --prefix="${S}" \
+ --with-ccp4="${S}" \
+ --with-clipper="${EPREFIX}"/usr \
+ --with-fftw="${EPREFIX}"/usr \
+ --with-mmdb="${EPREFIX}"/usr \
+ CXX=$(tc-getCXX) \
+ || die
+ popd 2>/dev/null
+}
+
+src_compile() {
+ # fsplit is required for the programs
+ pushd lib/src 2>/dev/null
+ emake fsplit -j1 || die
+ popd 2>/dev/null
+
+ # We do this manually, since disabling the clipper libraries also
+ # disables the clipper programs
+ pushd src/clipper_progs 2>/dev/null
+ emake || die
+ popd 2>/dev/null
+
+ emake -j1 || die "emake failed"
+}
+
+src_install() {
+ # Set up variables for build
+ source "${S}"/include/ccp4.setup-sh
+
+# make install || die "install failed"
+
+ # if we don't make this, a ton of programs fail to install
+ mkdir "${S}"/bin || die
+
+ # We do this manually, since disabling the clipper libraries also
+ # disables the clipper programs
+ pushd "${S}"/src/clipper_progs 2>/dev/null
+ emake install || die
+ popd 2>/dev/null
+
+ einstall || die "install failed"
+
+ # Fix env
+# -e "s~^\(.*setenv PYTHONPATH .*\)\${CCP4}.*~\1\${CCP4}/share/ccp4/python~g" \
+# -e "s~^\(.*export PYTHONPATH.*\)\${CCP4}.*~\1\${CCP4}/share/ccp4/python~g" \
+ sed -i \
+ -e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1${EPREFIX}/usr~g" \
+ -e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
+ -e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
+ -e "s~^\(setenv DBCCP4I_TOP\).*~\1 \$CCP4/share/ccp4/dbccp4i~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\$CCP4/share/ccp4/data/monomers/~g" \
+ -e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
+ -e "s~^\(.*setenv CLIB .*\)\$CCP4.*~\1\$CCP4/$(get_libdir)~g" \
+ -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
+ -e "s~^\(export CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \
+ -e "s~^\(export CCP4.*\$CCP4_MASTER\).*~\1~g" \
+ -e "s~^\(export CCP4I_TOP\).*~\1=\$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
+ -e "s~^\(export DBCCP4I_TOP\).*~\1=\$CCP4/share/ccp4/dbccp4i~g" \
+ -e "s~^\(.*export CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
+ -e "s~^\(.*export CLIBD.*\$CCP4\).*~\1/share/ccp4/data~g" \
+ -e "s~^\(.*export CLIBD_MON.*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
+ -e "s~^\(.*export MOLREPLIB.*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
+ -e "s~^\(.*export CLIB=.*\)\$CCP4.*~\1\$CCP4/$(get_libdir)~g" \
+ -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
+ -e "/IMOSFLM_VERSION/d" \
+ "${S}"/include/ccp4.setup* || die
+
+# -e "s~\$CCP4/share/XIAROOT/setup.sh~\$CCP4/share/ccp4/XIAROOT/setup.sh~g" \
+
+ # Don't check for updates on every sourcing of /etc/profile
+ sed -i \
+ -e "s:\(eval python.*\):#\1:g"
+ "${S}"/include/ccp4.setup* || die
+
+ # Collision with sci-chemistry/mrbump
+ rm -f "${S}"/bin/{mrbump,pydbviewer} || die
+
+ # Bins
+ exeinto /usr/libexec/ccp4/bin/
+ doexe "${S}"/bin/* || die
+
+ # Libs
+ for file in "${S}"/lib/*; do
+ if [[ -d ${file} ]]; then
+ continue
+ elif [[ -x ${file} ]]; then
+ dolib.so ${file} || die
+ else
+ insinto /usr/$(get_libdir)
+ doins ${file} || die
+ fi
+ done
+
+ sed \
+ -e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \
+ -i "${S}"/include/ccp4.setup-sh || die
+
+ # Setup scripts
+ insinto /etc/profile.d
+# newins "${S}"/include/ccp4.setup-bash ccp4.setup.bash || die
+ newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh || die
+# newins "${S}"/include/ccp4.setup-zsh ccp4.setup.zsh || die
+ newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh || die
+ rm -f "${S}"/include/ccp4.setup*
+
+ # Environment files, setup scripts, etc.
+ insinto /usr/share/ccp4/include
+ doins "${S}"/include/* || die
+
+ # smartie -- log parsing
+ insinto /usr/share/ccp4
+ doins -r "${S}"/share/smartie || die
+
+ # Install docs and examples
+ doman "${S}"/man/cat1/*
+
+ mv "${S}"/manual/README "${S}"/manual/README-manual
+ dodoc manual/* README CHANGES doc/* examples/README || die
+
+ rm "${D}"/usr/share/doc/${PF}/GNUmakefile.*
+ rm "${D}"/usr/share/doc/${PF}/COPYING.*
+
+ dohtml -r "${S}"/html/*
+
+ if use examples; then
+ for i in data rnase toxd; do
+ docinto examples/${i}
+ dodoc "${S}"/examples/${i}/*
+ done
+
+ docinto examples/tutorial
+ dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css
+ for i in data results; do
+ docinto examples/tutorial/${i}
+ dodoc "${S}"/examples/tutorial/${i}/*
+ done
+
+ for i in non-runnable runnable; do
+ docinto examples/unix/${i}
+ dodoc "${S}"/examples/unix/${i}/*
+ done
+ fi
+ # 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 -f "${D}"/usr/share/man/man1/rasmol.1* "${D}"/usr/lib/font84.dat || die
+
+ cat >> "${T}"/baubles <<- EOF
+ #!${EPREFIX}/bin/bash
+ exec $(PYTHON) \${CCP4}/share/ccp4/smartie/baubles.py
+ EOF
+
+ exeinto /usr/libexec/ccp4/bin/
+ doexe "${T}"/baubles || die
+}
+
+pkg_postinst() {
+ einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
+ einfo "in ${EPREFIX}/etc/profile.d/ccp4.setup* to modify this."
+}
+
+# Epatch wrapper for bulk patching
+ccp_patch() {
+ EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1}
+}
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