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AUX 6.1.3-clipper-template.patch 2619 SHA256 a185a93f76c23ce06256866cfaf0e9854a5702b95a1e49e4d3a5f732e0d1e2a3 SHA512 27d2e1eeace0ba7e690ac218ba4272e668e693b20292d2824831c6472627fcbf7013409a9255bd514918921cdc9ac98d86709ecda73b255230ccadc8d66e45a9 WHIRLPOOL f1e0694ec4a582cf1b547d845e8c8a86791aa3f109429f6a4aadfb30142719a07fee92d01f3e3a8f0703cc55833aae8fb6c3c2e8503efe741ac94276feb1b3b4
AUX 6.1.3-dont-build-balbes.patch 489 SHA256 dfe1b810fb07bf536528b9c955e3162dc470a803513ae6fa69848ed6d64503c4 SHA512 db5dba9eca411489baca16408e61bf3652087c238247a8128a39633b8e4a5dcf03931a55c07fa3887a9ee347ed9f7786a350468745258b65553a0e68d7cfb300 WHIRLPOOL 7b523121703f2ae87502dd411b48aa9bdba7e386d4365aa4c9b7de163ce134250c41a71e7fad9457601fea27a024a0d84588d1f937105c9384110ede8bcf25dc
DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c
EBUILD ccp4-apps-6.1.3-r11.ebuild 10006 SHA256 5a2ff857223827f942f61def95e35689422f736bc505d09396c1b0841676ad42 SHA512 2c40af7fb9ac79d4f8f14ed9aedd9afd770008bd5129e3aba116a8f495bb97260f7e322035cc8c68c02375a14b5b46171a7e0c06e2fa0bf5d448c2b43d05b4c2 WHIRLPOOL 8456c9b7bebdd97f16b1776ad42cd3a691af30291e34fdd9179d5f508a70d7d5e8618501adc20c7c9d78b6bbc35dda8d254c0d7281881a496f1ce30510e9bcec
EBUILD ccp4-apps-6.1.3-r12.ebuild 10063 SHA256 d7fd2c0e9b0de7949c7ccca39374be898179b88e036c729b5821fe1c959b8b73 SHA512 c2484cee98a08566ca7584bdb2230ec10a251154623521708b9b5651c9f37fa4087c5a4d91e9d6fdf0beaae579a246afa48b6db1101c2c6d7450a2673e67522d WHIRLPOOL 42ff9e4bff267c9489915adf3b482c25f01e0c2d8ba4e4526cf7eb5c76d610e6e533ac3fcc363ac09a07f2be3345bd4bb1669deb89612339ae14cf280f0f77ac
-MISC ChangeLog 7752 SHA256 d3132e8457b33c90a7ac8f46e6539b528e948cf4d7ee48d51a10aed7aec77aef SHA512 d5e486969863f15aebbaa0e6a58ebe581b3464d6131a49bf152774a71484dd882e64b92178800014d58adee89ba99b070dcd5f4b2d1b264aa473c48136d9d94f WHIRLPOOL 8d934227fb83bf30ee330f1023a000f5883827787441aea4ead3a6a4f0d69593fb3096bd7490e56fac13bbdb5baf79cf88723eb6d6e68f36c26d8de310849833
+EBUILD ccp4-apps-6.1.3-r13.ebuild 10018 SHA256 bcd8c275bbcd34356c24e3d8f7a43ea1772000fa4883052ccd5d55faa60d5b72 SHA512 dd6cc186feaa4d64f6c43e833631bf78704274e3b6bf5491d475fda1181f83e77d1b1023076a72bfa8ef24d90a52bb7d33640f07de7baf038c8252a6049abc6f WHIRLPOOL c1162051fe805c875d3eb40abe26b8fd73e069ac55140bc938cd18d18c7cd8eb953085f9cfbae07f890537f9d96f22d53c12ce22c0449f9f477adaa4e5e7267d
+MISC ChangeLog 7900 SHA256 e53043109e6c4d46dcc8fef72433ba001aecf59234f5c1e334c7ddf0b2b4ab67 SHA512 22df6b33a8839c5de9b78562a2aed7b1d91c99b082c0123242582b1692eb86f09b87163dcae43d5a0690146fad406230c7bf6633be77e35d3db9035d96e35d1c WHIRLPOOL 2b14cc8739d4ad72e834fc83e79bb3ab1604f80fe5a688975e4ba9f81ba2ffccb4feed2935ed6bc97ebc6f822f7c179c9b27531f52524b67f2021201e3aaba2d
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--- /dev/null
+# Copyright 1999-2015 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-r13.ebuild,v 1.1 2015/01/18 19:04:16 mgorny Exp $
+
+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}/${MY_P}-core-src.tar.gz
+ http://dev.gentooexperimental.org/~jlec/distfiles/${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/${!NAME}"
+done
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples X"
+
+X11DEPS="
+ x11-libs/libX11
+ x11-libs/libXaw
+ x11-libs/libXt
+ x11-libs/libxdl_view"
+
+TKDEPS="
+ >=dev-lang/tk-8.3
+ >=dev-tcltk/blt-2.4
+ dev-tcltk/iwidgets
+ dev-tcltk/itcl
+ dev-tcltk/itk
+ >=dev-tcltk/tdom-0.8
+ dev-tcltk/tktreectrl"
+
+SCILIBS="
+ ~sci-libs/ccp4-libs-${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}
+}
projects / gentoo.git / commitdiff