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454 lines
14 KiB
454 lines
14 KiB
# Copyright 1999-2011 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ccp4-6.0.1-r1.ebuild,v 1.13 2011/06/21 16:05:14 jlec Exp $
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inherit eutils fortran-2 gnuconfig toolchain-funcs
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SRC="ftp://ftp.ccp4.ac.uk/ccp4"
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PATCH_TOT="12"
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PATCH1=( src/mmdb_app_
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chainsaw.cpp-11May2006.diff )
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PATCH2=( src
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anisoanl.f-r1.22-r1.24.diff )
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PATCH3=( src/sc_
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sc.f-r1.9-r1.9.2.1.diff )
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PATCH4=( src/sc_
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setup.fh-r1.5-r1.5.2.1.diff )
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PATCH5=( src
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contact.f-12June2006.diff )
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PATCH6=( ccp4i/tasks
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refmac5.tcl-r1.39.2.3-r1.42.diff )
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PATCH7=( src
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act.f-6July2006.diff )
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PATCH8=( src
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rotmat.f-17July2006.diff )
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PATCH9=( src/molrep_
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molrep.f-r1.28-r1.28.2.1.diff )
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PATCH10=( src
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cad.f-r1.70-r1.72.diff )
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PATCH11=( src
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mtztona4.f-r1.23-r1.24.diff )
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PATCH12=( src
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omit.f-r1.12-r1.13.diff )
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DESCRIPTION="Protein X-ray crystallography toolkit"
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HOMEPAGE="http://www.ccp4.ac.uk/"
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RESTRICT="mirror"
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SRC_URI="${SRC}/${PV}/packed/${P}-core-src.tar.gz"
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for i in $(seq $PATCH_TOT); do
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NAME="PATCH${i}[1]"
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SRC_URI="${SRC_URI}
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${SRC}/${PV}/patches/${!NAME}"
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done
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LICENSE="ccp4"
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SLOT="0"
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KEYWORDS="ppc x86"
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IUSE="X"
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# app-office/sc overlaps sc binary and man page
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# We can't rename ours since the automated ccp4i interface expects it there,
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# as do many scripts. app-office/sc can't rename its because that's the name
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# of the package.
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RDEPEND="
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virtual/fortran
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>=dev-lang/tcl-8.3
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>=dev-lang/tk-8.3
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>=dev-tcltk/blt-2.4
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virtual/lapack
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virtual/blas
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=sci-libs/fftw-2*
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sci-chemistry/pdb-extract
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sci-chemistry/rasmol
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sci-libs/mccp4
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app-shells/tcsh
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!app-office/sc
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X? (
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x11-libs/libX11
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x11-libs/libXt
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x11-libs/libXaw
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)"
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DEPEND="${RDEPEND}
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X? (
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x11-misc/imake
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x11-proto/inputproto
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x11-proto/xextproto
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)"
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S="${WORKDIR}/${PN}-${PV}"
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src_unpack() {
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unpack ${A}
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cd "${S}"
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einfo "Applying upstream patches ..."
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for patch in $(seq $PATCH_TOT); do
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base="PATCH${patch}"
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dir=$(eval echo \${${base}[0]})
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p=$(eval echo \${${base}[1]})
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pushd ${dir} >& /dev/null
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ccp_patch "${DISTDIR}/${p}"
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popd >& /dev/null
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done
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einfo "Done."
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echo
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einfo "Applying Gentoo patches ..."
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# These two only needed when attempting to install outside build dir via
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# --bindir and --libdir instead of straight copying after build
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# it attempts to install some libraries during the build
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#ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch
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# hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
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# without this patch when --libdir is set
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# Rotgen still needs more patching to find it
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#ccp_patch "${FILESDIR}"/add-xdl-libdir.patch
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# it tries to create libdir, bindir etc on live system in configure
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ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
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# We already have sci-chemistry/rasmol
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ccp_patch "${FILESDIR}"/dont-build-rasmol.patch
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# We already have sci-chemistry/pdb-extract
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# Use configure option instead
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# ccp_patch "${FILESDIR}"/dont-build-pdb-extract.patch
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ccp_patch "${FILESDIR}"/create-mosflm-bindir.patch
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ccp_patch "${FILESDIR}"/make-mosflm-libdir.patch
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ccp_patch "${FILESDIR}"/make-mosflm-index-libdir.patch
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ccp_patch "${FILESDIR}"/make-mosflm-cbf-libdir.patch
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ccp_patch "${FILESDIR}"/make-ipmosflm-dir.patch
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# Don't use these when we aren't building phaser
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# ccp_patch "${FILESDIR}"/make-phaser-bindir.patch
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# ccp_patch "${FILESDIR}"/no-phaser-ld-assume-kernel.patch
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# # scons config.py tries to chmod python on live system
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# ccp_patch "${FILESDIR}"/dont-chmod-python-binary.patch
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# Don't use this when we aren't building clipper
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# For some reason clipper check for $enableval even when --enable is passed
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ccp_patch "${FILESDIR}"/pass-clipper-enablevals.patch
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ccp_patch "${FILESDIR}"/clipper-find-mccp4-includes.patch
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# Default to firefox browser, not 'netscape'
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ccp_patch "${FILESDIR}"/ccp4i-default-to-firefox.patch
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# Also use -lpthread when linking blas and lapack
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# We may need more fixing to use libcblas for the C files
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ccp_patch "${FILESDIR}"/check-blas-lapack-pthread.patch
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# gerror_ gets defined twice on ppc if you're using gfortran/g95
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ccp_patch "${FILESDIR}"/${PV}-ppc-double-define-gerror.patch
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einfo "Done." # done applying Gentoo patches
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echo
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gnuconfig_update
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}
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src_compile() {
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# Build system is broken if we set LDFLAGS
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unset LDFLAGS
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# GENTOO_OSNAME can be one of:
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# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
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# linux_compaq_compilers linux_intel_compilers generic Darwin
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# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
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if [[ "$(tc-getFC)" = "ifort" ]]; then
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if use ia64; then
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GENTOO_OSNAME="ia64_linux_intel"
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else
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# Should be valid for x86, maybe amd64
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GENTOO_OSNAME="linux_intel_compilers"
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fi
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else
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# Should be valid for x86 and amd64, at least
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GENTOO_OSNAME="linux"
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fi
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# Sets up env
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ln -s \
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ccp4.setup-bash \
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"${S}"/include/ccp4.setup
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# We agree to the license by emerging this, set in LICENSE
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sed -i \
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-e "s~^\(^agreed=\).*~\1yes~g" \
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"${S}"/configure
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# Fix up variables -- need to reset CCP4_MASTER at install-time
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sed -i \
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-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
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-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
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"${S}"/include/ccp4.setup*
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# Set up variables for build
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source "${S}"/include/ccp4.setup
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export CC=$(tc-getCC)
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export CXX=$(tc-getCXX)
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export COPTIM=${CFLAGS}
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export CXXOPTIM=${CXXFLAGS}
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# Default to -O2 if FFLAGS is unset
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export FC=$(tc-getFC)
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export FOPTIM=${FFLAGS:- -O2}
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# Can't use econf, configure rejects unknown options like --prefix
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./configure \
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$(use_enable X x) \
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--with-shared-libs \
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--with-fftw=/usr \
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--with-warnings \
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--disable-pdb_extract \
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--disable-cctbx \
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--disable-phaser \
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--tmpdir="${TMPDIR}" \
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${GENTOO_OSNAME} || die "econf failed"
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emake -j1 || die "emake failed"
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}
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src_install() {
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# Set up variables for build
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source "${S}"/include/ccp4.setup
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# Only needed when using --bindir and --libdir
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# Needed to avoid errors. Originally tried to make lib and bin
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# in configure script, now patched out by dont-make-dirs-in-configure.patch
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# dodir /usr/include /usr/$(get_libdir) /usr/bin
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# make install || die "install failed"
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einstall || die "install failed"
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# Fix env
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sed -i \
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-e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \
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-e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
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-e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
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-e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
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-e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \
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-e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \
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-e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \
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-e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \
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"${S}"/include/ccp4.setup*
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# Get rid of S instances
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# Also the main clipper library is built as libclipper-core, not libclipper
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sed -i \
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-e "s:${S}:usr:g" \
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-e "s:lclipper :lclipper-core :g" \
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"${S}"/bin/clipper-config
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# sed -i \
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# -e "s:${S}:usr:g" \
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# "${S}"/$(get_libdir)/cctbx/cctbx_build/setpaths*
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# Bins
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dobin "${S}"/bin/* || die
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# Libs
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for file in "${S}"/lib/*; do
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if [[ -d ${file} ]]; then
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continue
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elif [[ -x ${file} ]]; then
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dolib.so ${file} || die
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else
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insinto /usr/$(get_libdir)
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doins ${file} || die
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fi
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done
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# Fix libdir in all *.la files
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sed -i \
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-e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
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"${D}"/usr/$(get_libdir)/*.la
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# Library symlinks
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local LIBNAMES="libclipper-ccp4.so.0.0.0
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libclipper-cif.so.0.0.0
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libclipper-contrib.so.0.0.0
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libclipper-core.so.0.0.0
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libclipper-minimol.so.0.0.0
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libclipper-mmdbold.so.0.0.0
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libclipper-mmdb.so.0.0.0
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libclipper-mtz.so.1.0.0
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libclipper-phs.so.0.0.0
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libjwc_c.so.0.1.1
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libjwc_f.so.0.1.1
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libssm.so.0.0.0
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libxdl_viewextra.so.0.0.0
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libxdl_view.so.2.0.0"
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for LIBNAME in ${LIBNAMES}; do
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library_dosym ${LIBNAME}
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done
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# dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so
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# dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0
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# dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0.0
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#
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# dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so
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# dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0
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# dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0.0
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#
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# dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so
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# dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0
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# dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0.0
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#
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# dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so
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# dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0
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# dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0.0
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#
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# dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so
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# dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0
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# dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0.0
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#
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# dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so
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# dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0
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# dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0.0
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#
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# dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so
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# dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0
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# dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0.0
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#
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# dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so
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# dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1
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# dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1.0
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#
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# dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so
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# dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0
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# dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0.0
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#
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# dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so
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# dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0
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# dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0.1
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#
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# dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so
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# dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0
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# dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0.1
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#
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# dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so
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# dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0
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# dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0.0
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#
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# dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so
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# dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0
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# dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0.0
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#
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# dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so
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# dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2
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# dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2.0
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# Environment files, setup scripts, etc.
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insinto /usr/share/ccp4/include
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doins "${S}"/include/* || die
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# CCP4Interface - GUI
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insinto /usr/$(get_libdir)/ccp4
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doins -r "${S}"/ccp4i || die
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exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin
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doexe "${S}"/ccp4i/bin/* || die
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# Data
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insinto /usr/share/ccp4
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doins -r "${S}"/lib/data || die
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# Include files
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insinto /usr/include
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for i in ccp4 clipper mmdb ssm; do
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doins -r "${S}"/include/${i} || die
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done
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# Install docs and examples
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doman "${S}"/man/cat1/*
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mv "${S}"/manual/README "${S}"/manual/README-manual
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dodoc "${S}"/manual/*
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dodoc "${S}"/README "${S}"/CHANGES
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dodoc "${S}"/doc/*
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rm "${D}"/usr/share/doc/${PF}/GNUmakefile.gz
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rm "${D}"/usr/share/doc/${PF}/COPYING.gz
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dohtml -r "${S}"/html/*
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dodoc "${S}"/examples/README
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# Fix wrongly installed HTML pages from clipper
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dohtml "${D}"/usr/html/*
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rm -rf "${D}"/usr/html
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for i in data rnase toxd; do
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docinto examples/${i}
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dodoc "${S}"/examples/${i}/*
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done
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docinto examples/tutorial
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dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css
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for i in data results; do
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docinto examples/tutorial/${i}
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dodoc "${S}"/examples/tutorial/${i}/*
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done
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for i in non-runnable runnable; do
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docinto examples/unix/${i}
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dodoc "${S}"/examples/unix/${i}
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done
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# Needed for ccp4i docs to work
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dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples
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dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html
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# Fix overlaps with other packages
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rm "${D}"/usr/share/man/man1/rasmol.1*
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}
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pkg_postinst() {
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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
|
|
}
|