diff options
Diffstat (limited to 'sci-chemistry')
| -rw-r--r-- | sci-chemistry/ccp4-apps/ChangeLog | 6 | ||||
| -rw-r--r-- | sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r10.ebuild | 4 | ||||
| -rw-r--r-- | sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r9.ebuild | 378 |
3 files changed, 7 insertions, 381 deletions
diff --git a/sci-chemistry/ccp4-apps/ChangeLog b/sci-chemistry/ccp4-apps/ChangeLog index ac425a5cf5fc..b42e379a1627 100644 --- a/sci-chemistry/ccp4-apps/ChangeLog +++ b/sci-chemistry/ccp4-apps/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-chemistry/ccp4-apps # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.35 2012/04/14 09:49:05 nativemad Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.36 2012/04/26 15:46:31 jlec Exp $ + + 26 Apr 2012; Justin Lecher <jlec@gentoo.org> -ccp4-apps-6.1.3-r9.ebuild, + ccp4-apps-6.1.3-r10.ebuild: + Drop old 14 Apr 2012; Andreas Schuerch <nativemad@gentoo.org> ccp4-apps-6.1.3-r10.ebuild: diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r10.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r10.ebuild index 648dd5ca5980..cafa6ea88691 100644 --- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r10.ebuild +++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r10.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2012 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-r10.ebuild,v 1.8 2012/04/14 09:49:05 nativemad Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r10.ebuild,v 1.9 2012/04/26 15:46:31 jlec Exp $ EAPI=3 @@ -268,7 +268,7 @@ src_configure() { --disable-mosflm \ --disable-mrbump \ --tmpdir="${TMPDIR}" \ - ${GENTOO_OSNAME} || die "econf failed" + ${GENTOO_OSNAME} || die "configure failed" # We do this manually, since disabling the clipper libraries also # disables the clipper programs diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r9.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r9.ebuild deleted file mode 100644 index 6ce25bf7ecde..000000000000 --- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r9.ebuild +++ /dev/null @@ -1,378 +0,0 @@ -# Copyright 1999-2011 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-r9.ebuild,v 1.6 2011/10/08 08:40:36 jlec Exp $ - -EAPI=3 - -PYTHON_DEPEND="2" - -inherit autotools eutils fortran-2 flag-o-matic gnuconfig python 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 - 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 - virtual/fortran - !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_set_active_version 2 -} - -src_prepare() { - 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}"/${PV}-lapack.patch - - # Update things for oasis 4 usage - epatch "${WORKDIR}"/${PV}-oasis4.0.patch - sed 's: oasis : :g' -i src/Makefile.in || die - - einfo "Done." # done applying Gentoo patches - echo - - sed \ - -e "s:/usr:${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' \ - -i configure || 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 - - # 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_convert_shebangs $(python_get_version) src/ccp4_pipeline_simple.py ./share/smartie/*.py -} - -src_configure() { - # Build system is broken if we set LDFLAGS - export GENTOOLDFLAGS="${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 - - # 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* - - # 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-mosflm \ - --disable-mrbump \ - --tmpdir="${TMPDIR}" \ - ${GENTOO_OSNAME} || die "econf failed" - - # We do this manually, since disabling the clipper libraries also - # disables the clipper programs - pushd src/clipper_progs 2>/dev/null - econf \ - --prefix="${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 "${S}"/share/smartie || die - - # Install docs and examples - doman "${S}"/man/cat1/* - - 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/$(get_libdir)/ccp4/html || die - - # Fix overlaps with other packages - rm -f "${ED}"/usr/share/man/man1/rasmol.1* "${ED}"/usr/lib/font84.dat || die - mv "${ED}"/usr/share/man/man1/truncate{,-ccp4}.1 || die - mv "${ED}"/usr/share/man/man1/rapper{,-ccp4}.1 || die - mv "${ED}"/usr/share/man/man1/sc{,-ccp4}.1 || die - - cat >> "${T}"/baubles <<- EOF - #!${EPREFIX}/bin/bash - exec $(PYTHON) \${CCP4}/share/ccp4/smartie/baubles.py - EOF - - exeinto /usr/libexec/ccp4/bin/ - doexe "${T}"/baubles || die -} - -# Epatch wrapper for bulk patching -ccp_patch() { - EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} -} |