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Diffstat (limited to 'sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild')
-rw-r--r--sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild395
1 files changed, 0 insertions, 395 deletions
diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild
deleted file mode 100644
index 5e1032133922..000000000000
--- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild
+++ /dev/null
@@ -1,395 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools eutils fortran-2 flag-o-matic gnuconfig python-single-r1 toolchain-funcs
-
-MY_P="${PN/-apps}-${PV}"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-PATCH_TOT="0"
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-SRC_URI="
- ${SRC}/${PV}/${MY_P}-core-src.tar.gz
- https://dev.gentoo.org/~jlec/distfiles/${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} https://dev.gentoo.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/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE="examples X"
-
-X11DEPS="
- x11-libs/libX11
- x11-libs/libXaw
- x11-libs/libXt
- x11-libs/libxdl_view"
-
-TKDEPS="
- >=dev-lang/tk-8.3:0=
- >=dev-tcltk/blt-2.4
- dev-tcltk/iwidgets
- dev-tcltk/itcl
- dev-tcltk/itk
- >=dev-tcltk/tdom-0.8
- dev-tcltk/tktreectrl"
-
-SCILIBS="
- ~sci-libs/ccp4-libs-${PV}
- >=sci-libs/ccp4-libs-${PV}-r7
- sci-libs/clipper
- sci-libs/fftw:2.1
- sci-libs/mmdb:0
- sci-libs/ssm
- 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/libxml2:2
- dev-libs/libjwc_c
- dev-libs/libjwc_f
- dev-libs/boehm-gc
- !app-office/sc
- !<sci-chemistry/ccp4-6.1.3
- X? ( ${X11DEPS} )"
-DEPEND="${RDEPEND}
- X? (
- x11-misc/imake
- x11-proto/inputproto
- x11-proto/xextproto
- )"
-PDEPEND="${SCIAPPS}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
- fortran-2_pkg_setup
- python-single-r1_pkg_setup
-}
-
-src_prepare() {
- tc-export PKG_CONFIG
- 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
-
- # 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}"/${PV}-clipper-template.patch
-
- # Fix upstreams code
- ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
-
- # Not renaming, but unbundling libs
- ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch
-
- # Use pkg-config to detect BLAS/LAPCK
- ccp_patch "${FILESDIR}"/${PV}-lapack.patch
-
- # unbundle libs
- ccp_patch "${FILESDIR}"/${PV}-unbundle.patch
-
- # tcl-8.6
- ccp_patch "${FILESDIR}"/${P}-tcl8.6.patch
-
- # Update things for oasis 4 usage
- epatch "${WORKDIR}"/${PV}-oasis4.0.patch
- sed 's: oasis : :g' -i src/Makefile.in || die
-
- einfo "Done." # done applying Gentoo patches
- echo
-
- find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete
-
- sed \
- -e "s:/usr:${EPREFIX}/usr:g" \
- -e 's:-Wl,-rpath,$CLIB::g' \
- -e 's: -rpath $CLIB::g' \
- -e 's: -I${srcdir}/include/cpp_c_headers::g' \
- -e 's:sleep 1:sleep .2:g' \
- -e 's:\\$(XCIF_LIB):-L$srcdir/lib/ccif -lccif:g' \
- -e 's:\\$(XLAPACK_LIB):${XLAPACK_LIB}:g' \
- -e 's:\\$(CXX_LIBS):\${CXX_LIBS}:g' \
- -e 's:\\$(XLDFLAGS):\${XLDFLAGS}:g' \
- -i configure || die
-
- sed \
- -e '/o crunch2/s:$: ${XLAPACK_LIB}:g' \
- -i src/Makefile* || die
-
- find "${S}" -name "Makefile.*" \
- -exec sed -e 's|_FLAGS-|_FLAGS:-|g' -e "s:\(eval \$([[:alnum:]]*)\):\1 \$(GENTOOLDFLAGS):g" -i '{}' \;
-
- # Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version
- sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure || die
-
- # Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
- pushd src/rapper 2>/dev/null
- eautoreconf
- popd 2>/dev/null
-
- gnuconfig_update
-
- python_fix_shebang -f .
-}
-
-src_configure() {
- # Build system is broken if we set LDFLAGS
- export GENTOOLDFLAGS="${LDFLAGS}"
- unset LDFLAGS
-
- # These are broken with ./src/procheck/ps.f
- filter-flags "-floop-*"
-
- # GENTOO_OSNAME can be one of:
- # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
- # linux_compaq_compilers linux_intel_compilers generic Darwin
- # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
- if [[ "$(tc-getFC)" = "ifort" ]]; 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 || die
-
- # 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${EPREFIX}/usr/bin~g" \
- "${S}"/include/ccp4.setup* || die
-
- # Set up variables for build
- source "${S}"/include/ccp4.setup-sh
-
- export CC=$(tc-getCC)
- export CXX=$(tc-getCXX)
- export COPTIM=${CFLAGS}
- export CXXOPTIM=${CXXFLAGS}
- # Default to -O2 if FFLAGS is unset
- export FC=$(tc-getFC)
- export FOPTIM=${FFLAGS:- -O2}
- export BINSORT_SCR="${T}"
- export CCP4_MASTER="${WORKDIR}"
- export CCP4I_TCLTK="${EPREFIX}/usr/bin"
- export MAKE="make ${MAKEOPTS} ${EXTRA_EMAKE}"
-
- # 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-ssm \
- --disable-mosflm \
- --disable-mrbump \
- --tmpdir="${TMPDIR}" \
- ${GENTOO_OSNAME} || die "configure failed"
-
- # We do this manually, since disabling the clipper libraries also
- # disables the clipper programs
- pushd src/clipper_progs 2>/dev/null
- econf \
- --prefix="${S}" \
- --bindir="${ED}"/usr/libexec/ccp4/bin \
- --with-ccp4="${S}" \
- --with-clipper="${EPREFIX}/usr" \
- --with-fftw="${EPREFIX}/usr" \
- --with-mmdb="${EPREFIX}/usr" \
- CXX=$(tc-getCXX)
- 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 "${S}"/include/ccp4.setup-sh
-
- # if we don't make this, a ton of programs fail to install
- mkdir "${S}"/bin || die
-
- # We do this manually, since disabling the clipper libraries also
- # disables the clipper programs
- pushd "${S}"/src/clipper_progs 2>/dev/null
- emake install || die
- popd 2>/dev/null
-
- einstall || die "install failed"
-
- # Collision with sci-chemistry/mrbump
- rm -f "${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 ${file} || die
- fi
- done
-
- rm -f "${S}"/include/ccp4.setup*
-
- # smartie -- log parsing
- insinto /usr/share/ccp4
- doins -r "${S}"/share/smartie || die
-
- # Install docs and examples
- local _man
- pushd "${S}"/man/cat1 > /dev/null
- for _man in *; do
- newman ${_man} ${_man%??}-ccp4${_man:${#_man}-2:2}
- done
- popd > /dev/null
-
- mv "${S}"/manual/README "${S}"/manual/README-manual
- dodoc manual/* README CHANGES doc/* examples/README || die
-
- rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.*
- rm "${ED}"/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 || die
- dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die
-
- cat >> "${T}"/baubles <<- EOF
- #!${EPREFIX}/bin/bash
- exec "${EPYTHON}" "\${CCP4}/share/ccp4/smartie/baubles.py"
- EOF
-
- exeinto /usr/libexec/ccp4/bin/
- doexe "${T}"/baubles || die
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
- EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1}
-}