diff options
Diffstat (limited to 'sci-chemistry/ccp4-apps')
| -rw-r--r-- | sci-chemistry/ccp4-apps/ChangeLog | 8 | ||||
| -rw-r--r-- | sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r2.ebuild | 433 | ||||
| -rw-r--r-- | sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch | 14 |
3 files changed, 454 insertions, 1 deletions
diff --git a/sci-chemistry/ccp4-apps/ChangeLog b/sci-chemistry/ccp4-apps/ChangeLog index be9a832dc739..1aead97ca853 100644 --- a/sci-chemistry/ccp4-apps/ChangeLog +++ b/sci-chemistry/ccp4-apps/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-chemistry/ccp4-apps # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.3 2010/02/26 19:06:13 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.4 2010/03/28 13:42:22 jlec Exp $ + +*ccp4-apps-6.1.3-r2 (28 Mar 2010) + + 28 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> + +ccp4-apps-6.1.3-r2.ebuild: + balbes moved to sci-chemistry/balbes, fixed for PY3 26 Feb 2010; Justin Lecher (jlec) <jlec@j-schmitz.net> ccp4-apps-6.1.3-r1.ebuild: diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r2.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r2.ebuild new file mode 100644 index 000000000000..9ca9968d45ae --- /dev/null +++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r2.ebuild @@ -0,0 +1,433 @@ +# Copyright 1999-2010 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-r2.ebuild,v 1.1 2010/03/28 13:42:22 jlec Exp $ + +EAPI="2" + +PYTHON_DEPEND="2" + +inherit autotools eutils flag-o-matic fortran gnuconfig python toolchain-funcs + +FORTRAN="g77 gfortran ifc" + +MY_P="${PN/-apps}-${PV}" + +SRC="ftp://ftp.ccp4.ac.uk/ccp4" + +#UPDATE="04_03_09" +#PATCHDATE="090511" + +PATCH_TOT="0" +# Here's a little scriptlet to generate this list from the provided +# index.patches file +# +# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue; +# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done < +# index.patches +#PATCH1=( src/topp_ +#topp.f-r1.16.2.5-r1.16.2.6.diff ) +#PATCH2=( . +#configure-r1.372.2.18-r1.372.2.19.diff ) + +DESCRIPTION="Protein X-ray crystallography toolkit" +HOMEPAGE="http://www.ccp4.ac.uk/" +RESTRICT="mirror" +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/${!NAME}" +done + +LICENSE="ccp4" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="examples X" + +X11DEPS=" + x11-libs/libX11 + x11-libs/libXaw + x11-libs/libXt + x11-libs/libjwc_c + x11-libs/libjwc_f + x11-libs/libxdl_view" + +TKDEPS=" + >=dev-lang/tk-8.3 + >=dev-tcltk/blt-2.4 + dev-tcltk/iwidgets + dev-tcltk/itcl + dev-tcltk/itk + >=dev-tcltk/tdom-0.8 + dev-tcltk/tkimg + dev-tcltk/tktreectrl" + +SCILIBS=" + ~sci-libs/ccp4-libs-${PV} + sci-libs/clipper + =sci-libs/fftw-2* + sci-libs/mmdb + virtual/blas + virtual/lapack" + +SCIAPPS=" + sci-chemistry/pdb-extract + sci-chemistry/pymol + sci-chemistry/rasmol + sci-chemistry/oasis + balbes? ( sci-chemistry/balbes )" + +RDEPEND=" + ${TKDEPS} + ${SCILIBS} + app-shells/tcsh + dev-python/pyxml + dev-libs/libxml2 + dev-libs/boehm-gc + !app-office/sc + !<sci-chemistry/ccp4-6.1.2 + X? ( ${X11DEPS} )" +DEPEND="${RDEPEND} + =sys-devel/automake-1.6* + X? ( + x11-misc/imake + x11-proto/inputproto + x11-proto/xextproto + )" +PDEPEND="${SCIAPPS}" + +S="${WORKDIR}/${MY_P}" + +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 + + # coreutils installs a binary called truncate + ccp_patch "${FILESDIR}"/${PV}-rename-truncate.patch + mv ./doc/truncate.doc ./doc/ftruncate.doc || die + mv ./html/truncate.html ./html/ftruncate.html || die + + # conflicts with media-libs/raptor + ccp_patch "${FILESDIR}"/${PV}-rename-rapper.patch + mv ./doc/rapper.doc ./doc/rappermc.doc || die + mv ./html/rapper.html ./html/rappermc.html || die + + # 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}"/${PV}-clipper-template.patch + + # Update things for oasis 4 usage + epatch "${WORKDIR}"/${PV}-oasis4.0.patch + sed 's: oasis : :g' -i src/Makefile.in || die + + einfo "Done." # done applying Gentoo patches + echo + + # 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 + sed -i \ + -e '/^AC_CONFIG_SUBDIRS(\[gc7.0 libxml2\])/d' \ + configure.ac + sed -i \ + -e '/^SUBDIRS/s:libxml2 gc7.0::g' \ + Makefile.am + sed -i \ + -e '/^rappermc_LDADD/s:../gc7.0/libgc.la ../libxml2/libxml2.la:-lgc -lxml2:g' \ + LOOP/Makefile.am + sed -i \ + -e '/^INCLUDES/s:-I../gc7.0/include -I../libxml2/include:-I/usr/include/gc -I/usr/include/libxml2:g' \ + LOOP/Makefile.am + eautoreconf + popd 2>/dev/null + + gnuconfig_update + + python_convert_shebangs 2 src/ccp4_pipeline_simple.py +} + +src_configure() { + # Build system is broken if we set 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 [[ "${FORTRANC}" = "ifc" ]]; then + if use ia64; then + GENTOO_OSNAME="ia64_linux_intel" + else + # Should be valid for x86, maybe amd64 + GENTOO_OSNAME="linux_intel_compilers" + fi + else + # Should be valid for x86 and amd64, at least + GENTOO_OSNAME="linux" + fi + + # Sets up env + ln -s \ + ccp4.setup-bash \ + "${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~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ + -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \ + -e "s~^\(export CCP4I_TCLTK.*\)/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} + export BINSORT_SCR="${T}" + export CCP4_MASTER="${WORKDIR}" + export CCP4I_TCLTK="/usr/bin" + + # Can't use econf, configure rejects unknown options like --prefix + ./configure \ + $(use_enable X x) \ + --with-shared-libs \ + --with-fftw=/usr \ + --with-warnings \ + --disable-pdb_extract \ + --disable-cctbx \ + --disable-phaser \ + --disable-diffractionImg \ + --disable-clipper \ + --disable-mosflm \ + --disable-mrbump \ + --tmpdir="${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}" \ + --with-ccp4="${S}" \ + --with-clipper=/usr \ + --with-fftw=/usr \ + --with-mmdb=/usr \ + CXX=$(tc-getCXX) \ + || die + 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 "${S}"/include/ccp4.setup + +# make install || die "install failed" + + # if we don't make this, a ton of programs fail to install + mkdir "${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" + + # Fix env +# -e "s~^\(.*setenv PYTHONPATH .*\)\${CCP4}.*~\1\${CCP4}/share/ccp4/python~g" \ +# -e "s~^\(.*export PYTHONPATH.*\)\${CCP4}.*~\1\${CCP4}/share/ccp4/python~g" \ + 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~^\(setenv DBCCP4I_TOP\).*~\1 \$CCP4/share/ccp4/dbccp4i~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\$CCP4/share/ccp4/data/monomers/~g" \ + -e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \ + -e "s~^\(.*setenv CLIB .*\)\$CCP4.*~\1\$CCP4/$(get_libdir)~g" \ + -e "s~^\(export CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \ + -e "s~^\(export CCP4.*\$CCP4_MASTER\).*~\1~g" \ + -e "s~^\(export CCP4I_TOP\).*~\1=\$CCP4/$(get_libdir)/ccp4/ccp4i~g" \ + -e "s~^\(export DBCCP4I_TOP\).*~\1=\$CCP4/share/ccp4/dbccp4i~g" \ + -e "s~^\(.*export CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \ + -e "s~^\(.*export CLIBD.*\$CCP4\).*~\1/share/ccp4/data~g" \ + -e "s~^\(.*export CLIBD_MON.*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \ + -e "s~^\(.*export MOLREPLIB.*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \ + -e "s~^\(.*export CLIB=.*\)\$CCP4.*~\1\$CCP4/$(get_libdir)~g" \ + -e "/IMOSFLM_VERSION/d" \ + "${S}"/include/ccp4.setup* || die + +# -e "s~\$CCP4/share/XIAROOT/setup.sh~\$CCP4/share/ccp4/XIAROOT/setup.sh~g" \ + + # Don't check for updates on every sourcing of /etc/profile + sed -i \ + -e "s:\(eval python.*\):#\1:g" + "${S}"/include/ccp4.setup* || die + + # Collision with sci-chemistry/mrbump + rm -f "${S}"/bin/{mrbump,pydbviewer} || die + + # 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 ${file} || die + fi + done + + sed \ + -e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \ + -i "${S}"/include/ccp4.setup-sh || die + + # Setup scripts + insinto /etc/profile.d +# newins "${S}"/include/ccp4.setup-bash ccp4.setup.bash || die + newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh || die +# newins "${S}"/include/ccp4.setup-zsh ccp4.setup.zsh || die + newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh || die + rm -f "${S}"/include/ccp4.setup* + + # Environment files, setup scripts, etc. + insinto /usr/share/ccp4/include + doins "${S}"/include/* || die + + # smartie -- log parsing + insinto /usr/share/ccp4 + doins -r "${S}"/share/smartie || die + + # Install docs and examples + doman "${S}"/man/cat1/* + + mv "${S}"/manual/README "${S}"/manual/README-manual + dodoc manual/* README CHANGES doc/* examples/README || die + + rm "${D}"/usr/share/doc/${PF}/GNUmakefile.* + rm "${D}"/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 + dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html + + # Fix overlaps with other packages + rm -f "${D}"/usr/share/man/man1/rasmol.1* "${D}"/usr/lib/font84.dat || die + + cat >> "${T}"/baubles <<- EOF + #!/bin/bash + exec $(PYTHON) \${CCP4}/share/ccp4/smartie/baubles.py + EOF + + dobin "${T}"/baubles || die +} + +pkg_postinst() { + einfo "The Web browser defaults to firefox. Change CCP4_BROWSER" + einfo "in /etc/profile.d/ccp4.setup* to modify this." +} + +# Epatch wrapper for bulk patching +ccp_patch() { + EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} +} diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch new file mode 100644 index 000000000000..f1df3e5e19f9 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch @@ -0,0 +1,14 @@ +diff --git a/share/Makefile.in b/share/Makefile.in +index 2d4f20b..4500993 100755 +--- a/share/Makefile.in ++++ b/share/Makefile.in +@@ -18,9 +18,6 @@ install : + for i in $(MRBUMP_TARGETS); do \ + test -s $(MRBUMP_BINDIR)/$$i && $(INSTALL_PROGRAM) $(MRBUMP_BINDIR)/$$i $(bindir)/$$i || true ;\ + done +- for i in $(BALBES_TARGETS); do \ +- test -s $(BALBES_BINDIR)/$$i && $(INSTALL_PROGRAM) $(BALBES_BINDIR)/$$i $(bindir)/$$i || true ;\ +- done + + clean : ; -rm -f core *.o *~ a.out + |