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gentoo-overlay/sci-chemistry/ccp4/ccp4-6.0.1-r1.ebuild

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# Copyright 1999-2011 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-r1.ebuild,v 1.13 2011/06/21 16:05:14 jlec Exp $
inherit eutils fortran-2 gnuconfig toolchain-funcs
SRC="ftp://ftp.ccp4.ac.uk/ccp4"
PATCH_TOT="12"
PATCH1=( src/mmdb_app_
chainsaw.cpp-11May2006.diff )
PATCH2=( src
anisoanl.f-r1.22-r1.24.diff )
PATCH3=( src/sc_
sc.f-r1.9-r1.9.2.1.diff )
PATCH4=( src/sc_
setup.fh-r1.5-r1.5.2.1.diff )
PATCH5=( src
contact.f-12June2006.diff )
PATCH6=( ccp4i/tasks
refmac5.tcl-r1.39.2.3-r1.42.diff )
PATCH7=( src
act.f-6July2006.diff )
PATCH8=( src
rotmat.f-17July2006.diff )
PATCH9=( src/molrep_
molrep.f-r1.28-r1.28.2.1.diff )
PATCH10=( src
cad.f-r1.70-r1.72.diff )
PATCH11=( src
mtztona4.f-r1.23-r1.24.diff )
PATCH12=( src
omit.f-r1.12-r1.13.diff )
DESCRIPTION="Protein X-ray crystallography toolkit"
HOMEPAGE="http://www.ccp4.ac.uk/"
RESTRICT="mirror"
SRC_URI="${SRC}/${PV}/packed/${P}-core-src.tar.gz"
for i in $(seq $PATCH_TOT); do
NAME="PATCH${i}[1]"
SRC_URI="${SRC_URI}
${SRC}/${PV}/patches/${!NAME}"
done
LICENSE="ccp4"
SLOT="0"
KEYWORDS="ppc x86"
IUSE="X"
# app-office/sc overlaps sc binary and man page
# We can't rename ours since the automated ccp4i interface expects it there,
# as do many scripts. app-office/sc can't rename its because that's the name
# of the package.
RDEPEND="
virtual/fortran
>=dev-lang/tcl-8.3
>=dev-lang/tk-8.3
>=dev-tcltk/blt-2.4
virtual/lapack
virtual/blas
=sci-libs/fftw-2*
sci-chemistry/pdb-extract
sci-chemistry/rasmol
sci-libs/mccp4
app-shells/tcsh
!app-office/sc
X? (
x11-libs/libX11
x11-libs/libXt
x11-libs/libXaw
)"
DEPEND="${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}"/${PV}-ppc-double-define-gerror.patch
einfo "Done." # done applying Gentoo patches
echo
gnuconfig_update
}
src_compile() {
# Build system is broken if we set LDFLAGS
unset LDFLAGS
# GENTOO_OSNAME can be one of:
# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
# linux_compaq_compilers linux_intel_compilers generic Darwin
# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
if [[ "$(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
# 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=$(tc-getFC)
export FOPTIM=${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
}
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