sci-chemistry/ccp4/ccp4-6.0.2.ebuild - chromiumos/overlays/portage - Git at Google

 # Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ccp4-6.0.2.ebuild,v 1.7 2009/03/04 13:41:43 loki_val Exp $

 inherit fortran eutils gnuconfig toolchain-funcs

 FORTRAN="g77 gfortran ifc"

 SRC="ftp://ftp.ccp4.ac.uk/ccp4"

 PATCH_TOT="0"
 #PATCH1=( src/mmdb_app_
 #	chainsaw.cpp-11May2006.diff )
 #PATCH2=( src
 #	anisoanl.f-r1.22-r1.24.diff )

 DESCRIPTION="Protein X-ray crystallography toolkit"
 HOMEPAGE="http://www.ccp4.ac.uk/"
 RESTRICT="mirror"
 SRC_URI="${SRC}/${PV}/source/${P}-core-src.tar.gz"
 for i in $(seq $PATCH_TOT); do
 	NAME="PATCH${i}[1]"
 	SRC_URI="${SRC_URI}
 		${SRC}/${PV}/patches/${!NAME}"
 done
 LICENSE="ccp4"
 SLOT="0"
 KEYWORDS="~ppc ~x86"
 IUSE="X"
 # app-office/sc overlaps sc binary and man page
 # We can't rename ours since the automated ccp4i interface expects it there,
 # as do many scripts. app-office/sc can't rename its because that's the name
 # of the package.
 RDEPEND="X? (
 				x11-libs/libX11
 				x11-libs/libXt
 				x11-libs/libXaw
 		)
 		>=dev-lang/tcl-8.3
 		>=dev-lang/tk-8.3
 		>=dev-tcltk/blt-2.4
 		virtual/lapack
 		virtual/blas
 		=sci-libs/fftw-2*
 		sci-chemistry/pdb-extract
 		sci-chemistry/rasmol
 		sci-libs/mccp4
 		app-shells/tcsh
 		!app-office/sc"
 DEPEND="${RDEPEND}
 		X? (
 				x11-misc/imake
 				x11-proto/inputproto
 				x11-proto/xextproto
 		)"

 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() {
 	# Build system is broken if we set LDFLAGS
 	unset LDFLAGS

 	# 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}

 	# 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() {
 	# Set up variables for build
 	source ${S}/include/ccp4.setup

 # 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:${S}:$usr:g" \
 		-e "s:lclipper :lclipper-core :g" \
 		${S}/bin/clipper-config
 #	sed -i \
 #		-e "s:${S}:usr:g" \
 #		${S}/$(get_libdir)/cctbx/cctbx_build/setpaths*

 	# Bins
 	dobin ${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

 	# 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.
 	insinto /usr/share/ccp4/include
 	doins ${S}/include/* || die

 	# CCP4Interface - GUI
 	insinto /usr/$(get_libdir)/ccp4
 	doins -r ${S}/ccp4i || die
 	exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin
 	doexe ${S}/ccp4i/bin/* || die

 	# Data
 	insinto /usr/share/ccp4
 	doins -r ${S}/lib/data || die

 	# Include files
 	insinto /usr/include
 	for i in ccp4 clipper mmdb ssm; do
 		doins -r ${S}/include/${i} || die
 	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
 		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

 	# 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*
 }

 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
 }
	# Copyright 1999-2009 Gentoo Foundation
	# Distributed under the terms of the GNU General Public License v2
	# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ccp4-6.0.2.ebuild,v 1.7 2009/03/04 13:41:43 loki_val Exp $

	inherit fortran eutils gnuconfig toolchain-funcs

	FORTRAN="g77 gfortran ifc"

	SRC="ftp://ftp.ccp4.ac.uk/ccp4"

	PATCH_TOT="0"
	#PATCH1=( src/mmdb_app_
	# chainsaw.cpp-11May2006.diff )
	#PATCH2=( src
	# anisoanl.f-r1.22-r1.24.diff )

	DESCRIPTION="Protein X-ray crystallography toolkit"
	HOMEPAGE="http://www.ccp4.ac.uk/"
	RESTRICT="mirror"
	SRC_URI="${SRC}/${PV}/source/${P}-core-src.tar.gz"
	for i in $(seq $PATCH_TOT); do
	NAME="PATCH${i}[1]"
	SRC_URI="${SRC_URI}
	${SRC}/${PV}/patches/${!NAME}"
	done
	LICENSE="ccp4"
	SLOT="0"
	KEYWORDS="~ppc ~x86"
	IUSE="X"
	# app-office/sc overlaps sc binary and man page
	# We can't rename ours since the automated ccp4i interface expects it there,
	# as do many scripts. app-office/sc can't rename its because that's the name
	# of the package.
	RDEPEND="X? (
	x11-libs/libX11
	x11-libs/libXt
	x11-libs/libXaw
	)
	>=dev-lang/tcl-8.3
	>=dev-lang/tk-8.3
	>=dev-tcltk/blt-2.4
	virtual/lapack
	virtual/blas
	=sci-libs/fftw-2*
	sci-chemistry/pdb-extract
	sci-chemistry/rasmol
	sci-libs/mccp4
	app-shells/tcsh
	!app-office/sc"
	DEPEND="${RDEPEND}
	X? (
	x11-misc/imake
	x11-proto/inputproto
	x11-proto/xextproto
	)"

	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() {
	# Build system is broken if we set LDFLAGS
	unset LDFLAGS

	# 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}

	# 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() {
	# Set up variables for build
	source ${S}/include/ccp4.setup

	# 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:${S}:$usr:g" \
	-e "s:lclipper :lclipper-core :g" \
	${S}/bin/clipper-config
	# sed -i \
	# -e "s:${S}:usr:g" \
	# ${S}/$(get_libdir)/cctbx/cctbx_build/setpaths*

	# Bins
	dobin ${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

	# 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.
	insinto /usr/share/ccp4/include
	doins ${S}/include/* \|\| die

	# CCP4Interface - GUI
	insinto /usr/$(get_libdir)/ccp4
	doins -r ${S}/ccp4i \|\| die
	exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin
	doexe ${S}/ccp4i/bin/* \|\| die

	# Data
	insinto /usr/share/ccp4
	doins -r ${S}/lib/data \|\| die

	# Include files
	insinto /usr/include
	for i in ccp4 clipper mmdb ssm; do
	doins -r ${S}/include/${i} \|\| die
	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
	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

	# 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*
	}

	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
	}