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author | Justin Lecher <jlec@gentoo.org> | 2010-02-06 00:37:43 +0000 |
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committer | Justin Lecher <jlec@gentoo.org> | 2010-02-06 00:37:43 +0000 |
commit | 571e1f99857556e2876532f37882336f5bd72be1 (patch) | |
tree | ecee8dc95498811153f952164fd0c05a2ea55551 /sci-chemistry/ccp4-apps | |
parent | Automated update of use.local.desc (diff) | |
download | gentoo-2-571e1f99857556e2876532f37882336f5bd72be1.tar.gz gentoo-2-571e1f99857556e2876532f37882336f5bd72be1.tar.bz2 gentoo-2-571e1f99857556e2876532f37882336f5bd72be1.zip |
splitted apps from ccp4
(Portage version: 2.2_rc62/cvs/Linux x86_64)
Diffstat (limited to 'sci-chemistry/ccp4-apps')
19 files changed, 1445 insertions, 0 deletions
diff --git a/sci-chemistry/ccp4-apps/ChangeLog b/sci-chemistry/ccp4-apps/ChangeLog new file mode 100644 index 000000000000..924db5f31ccd --- /dev/null +++ b/sci-chemistry/ccp4-apps/ChangeLog @@ -0,0 +1,20 @@ +# 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 1.1 2010/02/06 00:37:43 jlec Exp $ + +*ccp4-apps-6.1.3 (06 Feb 2010) + + 06 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org> + +files/6.1.3-clipper-mmdbold-ggc-4.3.patch, + +files/6.1.3-clipper-template.patch, + +files/6.1.3-dont-build-double-and-make-bindir.patch, + +files/6.1.3-dont-build-imosflm.patch, +files/6.1.3-dont-build-libs.patch, + +files/6.1.3-dont-build-molref.patch, +files/6.1.3-dont-build-scala.patch, + +files/6.1.3-dont-build-xia.patch, +files/6.1.3-dont-configure.patch, + +files/6.1.3-dont-make-dirs-in-configure.patch, + +files/6.1.3-fix-setup-bash-incompatibility.patch, + +files/6.1.3-pisa.patch, +files/6.1.3-pythonpath.patch, + +files/6.1.3-rename-rapper.patch, +files/6.1.3-rename-truncate.patch, + +files/6.1.3-setup.patch, +ccp4-apps-6.1.3.ebuild, +metadata.xml: + Splitted apps from ccp4 + diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3.ebuild new file mode 100644 index 000000000000..d1d462078ae7 --- /dev/null +++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3.ebuild @@ -0,0 +1,431 @@ +# 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.ebuild,v 1.1 2010/02/06 00:37:43 jlec Exp $ + +EAPI="2" + +inherit fortran eutils flag-o-matic gnuconfig toolchain-funcs autotools + +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* + virtual/blas + virtual/lapack" + +SCIAPPS=" + sci-chemistry/pdb-extract + sci-chemistry/pymol + sci-chemistry/rasmol + sci-chemistry/oasis" + +RDEPEND="X? ( ${X11DEPS} ) + ${TKDEPS} + ${SCILIBS} + app-shells/tcsh + dev-python/pyxml + dev-libs/libxml2 + dev-libs/boehm-gc + !app-office/sc + !<sci-chemistry/ccp4-6.1.2" +DEPEND="${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 + + # molref is provided as binary and dynamically linked against icc + ccp_patch "${FILESDIR}"/${PV}-dont-build-molref.patch + + # no xia + ccp_patch "${FILESDIR}"/${PV}-dont-build-xia.patch + + # We build scala ourself + ccp_patch "${FILESDIR}"/${PV}-dont-build-scala.patch + + # We build scala ourself + ccp_patch "${FILESDIR}"/${PV}-dont-build-imosflm.patch + + # 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 binaries available from the standalone version + sed -i -e "/^REFMACTARGETS/s:refmac5 libcheck makecif molrep sfcheck::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 +} + +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~^\(export CCP4_MASTER.*\)${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 "/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-clipper-mmdbold-ggc-4.3.patch b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-mmdbold-ggc-4.3.patch new file mode 100644 index 000000000000..66186609a668 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-mmdbold-ggc-4.3.patch @@ -0,0 +1,22 @@ +--- ccp4-6.0.99e.orig/lib/clipper/clipper/mmdbold/clipper_mmdb.cpp 2008-07-31 13:23:13.000000000 -0700 ++++ ccp4-6.0.99e/lib/clipper/clipper/mmdbold/clipper_mmdb.cpp 2008-07-31 13:47:35.000000000 -0700 +@@ -43,7 +43,7 @@ + + #include <set> + #include <algorithm> +- ++#include <string.h> + + namespace clipper { + +--- ccp4-6.0.99e.orig/lib/clipper/clipper/mmdbold/clipper_mmdb_wrapper.cpp.orig 2008-07-31 13:49:53.000000000 -0700 ++++ ccp4-6.0.99e/lib/clipper/clipper/mmdbold/clipper_mmdb_wrapper.cpp 2008-07-31 13:50:25.000000000 -0700 +@@ -40,7 +40,7 @@ + //L MA 02111-1307 USA + + #include "clipper_mmdb_wrapper.h" +- ++#include <string.h> + + namespace clipper { + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch new file mode 100644 index 000000000000..433a78dbd23b --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch @@ -0,0 +1,70 @@ +--- src/clipper_progs/src/intensity_target.h.orig 2010-01-21 11:27:13.236795886 -0600 ++++ src/clipper_progs/src/intensity_target.h 2010-01-21 11:31:33.450686927 -0600 +@@ -70,9 +70,31 @@ + { + public: + //! constructor: takes the datalist against which to calc target +- TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ); ++ TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ) ++ { ++ hkl_data1 = &hkl_data1_; ++ hkl_data2 = &hkl_data2_; ++ } + //! return the value and derivatives of the target function +- Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const; ++ Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const ++ { ++ Rderiv result; ++ result.r = result.dr = result.dr2 = 0.0; ++ const T1& it1 = (*hkl_data1)[ih]; ++ const T2& it2 = (*hkl_data2)[ih]; ++ if ( !it1.missing() && !it2.missing() ) ++ if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) { ++ const ftype eps = ih.hkl_class().epsilon(); ++ const ftype i1 = it1.I() / eps; ++ const ftype i2 = it2.I() / eps; ++ const ftype w = sqrt( i1 * i2 ); ++ const ftype d = intensityh + log(i1) - log(i2); ++ result.r = w * d * d; ++ result.dr = 2.0 * w * d; ++ result.dr2 = 2.0 * w; ++ } ++ return result; ++ } + //! the type of the function: optionally used to improve convergence + FNtype type() const { return QUADRATIC; } + private: +@@ -109,33 +131,4 @@ + return result; + } + +- // Log I1-I2 scaling +- +- template<class T1, class T2> TargetFn_scaleLogI1I2<T1,T2>::TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ) +- { +- hkl_data1 = &hkl_data1_; +- hkl_data2 = &hkl_data2_; +- } +- +- template<class T1, class T2> TargetFn_base::Rderiv TargetFn_scaleLogI1I2<T1,T2>::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const +- { +- Rderiv result; +- result.r = result.dr = result.dr2 = 0.0; +- const T1& it1 = (*hkl_data1)[ih]; +- const T2& it2 = (*hkl_data2)[ih]; +- if ( !it1.missing() && !it2.missing() ) +- if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) { +- const ftype eps = ih.hkl_class().epsilon(); +- const ftype i1 = it1.I() / eps; +- const ftype i2 = it2.I() / eps; +- const ftype w = sqrt( i1 * i2 ); +- const ftype d = intensityh + log(i1) - log(i2); +- result.r = w * d * d; +- result.dr = 2.0 * w * d; +- result.dr2 = 2.0 * w; +- } +- return result; +- } +- +- + #endif diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch new file mode 100644 index 000000000000..e62ae12adfbe --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch @@ -0,0 +1,24 @@ +--- ccp4-6.1.1/x-windows/Makefile.in 2008-08-11 19:20:01.000000000 +0200 ++++ ccp4-6.1.1/x-windows/Makefile.in.new 2009-02-27 14:32:25.000000000 +0100 +@@ -35,7 +35,7 @@ + # + # all + # +-all : xdlview libjwc_c libjwc_f rotgen_ hklview xjiffy rasmol2 ipmosflm ++all : rotgen_ hklview xjiffy + # + # xdl_view + # +@@ -157,11 +157,10 @@ + # + install_obj = hklview rotgen ipmosflm + install: all ++ mkdir -p $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir) + cd $(srcdir)/XCCPJIFFY ; $(MAKE) bindir=$(bindir) libdir=$(libdir) install +- $(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir) + cd $(rotgen_dir); $(MAKE) install +- $(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir) + # + # clean + # diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch new file mode 100644 index 000000000000..f645643e1c67 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch @@ -0,0 +1,11 @@ +--- ccp4i/Makefile.in 2009-06-19 15:08:53.000000000 +0200 ++++ ccp4i/Makefile.in.new 2009-08-04 21:10:14.000000000 +0200 +@@ -9,7 +9,7 @@ + SHELL = /bin/sh + DESTDIR = $(prefix) + CCP4I_BINDIR = $(top_srcdir)/ccp4i/bin +-CCP4I_TARGETS = ccp4i imosflm loggraph crank mapslicer ++CCP4I_TARGETS = ccp4i loggraph crank mapslicer + + install : + for i in $(CCP4I_TARGETS); do \ diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch new file mode 100644 index 000000000000..315006508883 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch @@ -0,0 +1,35 @@ +--- Makefile.in 2009-06-19 15:13:29.000000000 +0200 ++++ Makefile.in.new 2009-08-02 23:06:41.000000000 +0200 +@@ -2,7 +2,7 @@ + # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch,v 1.1 2010/02/06 00:37:40 jlec Exp $ + + SHELL = /bin/sh +-DIRS = $(fftwdir) $(clipperdir) $(diffimdir) $(lapackdir) $(ccifdir) lib/src $(ssmdir) src lib/data unsupported/src x-windows share ccp4i $(prereleasedir) ++DIRS = src lib/data unsupported/src x-windows share ccp4i $(prereleasedir) + # this is for the benefit of makes that don't pass variable values in + # recursive invocations, so that you can override these values on the + # command line at the top level +@@ -69,19 +69,19 @@ + $(MAKE) -i $(MFLAGS) $(MVARS) install; else true; fi ; \ + $(MAKE) install + +-srcdir : FORCE libdir ++srcdir : FORCE + if test -d src; then cd src; $(MAKE) $(MFLAGS) $(MVARS); else true; fi + + supported : srcdir + +-unsupported : FORCE libdir ++unsupported : FORCE + if test -d unsupported/src; then cd unsupported/src; \ + $(MAKE) $(MFLAGS) $(MVARS); else true; fi + +-datadir : FORCE libdir ++datadir : FORCE + cd lib/data; $(MAKE) $(MFLAGS) $(MVARS) + +-xwindir : FORCE libdir ++xwindir : FORCE + if test -f x-windows/Makefile; then cd x-windows; \ + $(MAKE) -i $(MFLAGS) ; else true; fi + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch new file mode 100644 index 000000000000..f16b0ecb938c --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch @@ -0,0 +1,19 @@ +--- src/pisa/Makefile.am 2007-07-10 10:56:05.000000000 +0200 ++++ src/pisa/Makefile.am.new 2009-06-11 21:16:51.000000000 +0200 +@@ -1,4 +1,4 @@ +-SUBDIRS = molref pisastore sbase ++SUBDIRS = pisastore sbase + + pkgdatadir = $(datadir)/pisa + +--- src/pisa/Makefile.in 2009-06-12 21:12:08.000000000 +0200 ++++ src/pisa/Makefile.in.new 2009-06-12 21:41:52.000000000 +0200 +@@ -82,7 +82,7 @@ + am__quote = @am__quote@ + install_sh = @install_sh@ + pisa_LDFLAGS = @pisa_LDFLAGS@ +-SUBDIRS = molref pisastore sbase ++SUBDIRS = pisastore sbase + + dist_pkgdata_DATA = pisa.cfg + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch new file mode 100644 index 000000000000..af4fd8219c4f --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch @@ -0,0 +1,42 @@ +--- ./src/Makefile.in 2009-03-20 15:06:41.000000000 +0100 ++++ ./src/Makefile.in.new 2009-07-31 23:46:13.000000000 +0200 +@@ -50,7 +50,7 @@ + + # these live in subdirectories and have more than one dependency: + OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \ +- scala dm dmmulti stereo mapmask maprot ncsmask \ ++ dm dmmulti stereo mapmask maprot ncsmask \ + sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \ + anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat + +@@ -637,7 +637,7 @@ + + ### scala, mapmask, maprot, ncsmask, combat + +-scala mapmask maprot ncsmask combat sc dyndom: # dependencies below ++mapmask maprot ncsmask combat sc dyndom: # dependencies below + @$(SETFLAGS) pwd=`pwd` ; rm -f $@; \ + cd $(srcdir)/$@_; \ + echo $(FC) $${$@_FLAGS-"$(FFLAGS)"} -c -o $$pwd/$@.o `pwd`/$@.f ;\ +@@ -1002,21 +1002,6 @@ + proclean: $(srcdir)/procheck/clean.f $(srcdir)/procheck/brkcln.par + rmsdev: $(srcdir)/procheck/rmsdev.f $(srcdir)/procheck/rmsdev.inc + +-scaladir = $(srcdir)/scala_ +-scala : $(scaladir)/scala.f $(scaladir)/column.fh $(scaladir)/orient.fh \ +- $(scaladir)/params.fh $(scaladir)/rfile.fh $(scaladir)/scales.fh \ +- $(scaladir)/nbtchc.fh $(scaladir)/parameter.fh $(scaladir)/refcon.fh \ +- $(scaladir)/rundef.fh $(scaladir)/sdfacc.fh $(scaladir)/flags.fh \ +- $(scaladir)/inout.fh $(scaladir)/dump.fh $(scaladir)/tie.fh \ +- $(scaladir)/outcon.fh $(scaladir)/version.fh $(scaladir)/anomtc.fh \ +- $(scaladir)/axes.fh $(scaladir)/bigarg.fh \ +- $(scaladir)/errors.fh $(scaladir)/flow.fh $(scaladir)/glocon.fh \ +- $(scaladir)/means.fh $(scaladir)/refflg.fh $(scaladir)/stats.fh \ +- $(scaladir)/symmty.fh $(scaladir)/sharvest.fh $(scaladir)/chtml.fh \ +- $(scaladir)/htmbuf.fh $(scaladir)/sphhrm.fh $(scaladir)/crlncf.fh \ +- $(scaladir)/datasets.fh $(scaladir)/dts_storage.fh \ +- $(scaladir)/sclinimeans.fh $(scaladir)/timecor.fh +- + freemask.o: $(dmdir)/freemask.f $(dmdir)/crystal.fh $(dmdir)/cycl.fh \ + $(dmdir)/dmheader.fh $(dmdir)/io.fh $(dmdir)/output.fh \ + $(dmdir)/params.fh $(dmdir)/uvwdata.fh diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch new file mode 100644 index 000000000000..3af4af503fa6 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch @@ -0,0 +1,14 @@ +--- src/Makefile.in 2009-07-05 16:50:25.000000000 +0200 ++++ src/Makefile.in.new 2009-07-05 19:38:06.000000000 +0200 +@@ -50,9 +50,9 @@ + + # these live in subdirectories and have more than one dependency: + OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \ +- scala dm dmmulti stereo mapmask maprot ncsmask chef \ ++ scala dm dmmulti stereo mapmask maprot ncsmask \ + sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \ +- anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat ++ anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf + + # targets built from .c sources: + CSIMPLE = pltdev binsort diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch new file mode 100644 index 000000000000..1e59578473ff --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch @@ -0,0 +1,111 @@ +--- configure 2009-08-07 12:11:28.000000000 +0200 ++++ configure.new.nolib 2009-08-17 22:30:39.000000000 +0200 +@@ -3113,41 +3113,6 @@ + RX_L="$configdir/lib/rxdispencer/rx" + export RX_H RX_L + fi +- echo +- echo "Running separate configure for CCIF library." +- echo +- cd lib/ccif +- echo "Updating modification times for configuration files" +- echo "Please wait..." +- for i in configure.in aclocal.m4 configure Makefile.in; do +- touch $i && sleep 1 +- done +- echo "...done." +- +- if [ "X$LIBFOPTIM" != "X" ]; then +- FOPTIM_save=$FOPTIM +- FOPTIM=$LIBFOPTIM +- FFLAGS="${FOPTIM} ${XFFLAGS}" +- fi +- if [ "X$LIBCOPTIM" != "X" ]; then +- COPTIM_save=$COPTIM +- COPTIM=$LIBCOPTIM +- CFLAGS="${COPTIM} ${XCFLAGS}" +- fi +- ( touch /tmp/$$.cache_file 2>/dev/null && \ +- cat /dev/null > /tmp/$$.cache_file && \ +- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file ) || \ +- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif +- rm -f /tmp/$$.cache_file +- if [ "X$LIBFOPTIM" != "X" ]; then +- FOPTIM=$FOPTIM_save +- FFLAGS="${FOPTIM} ${XFFLAGS}" +- fi +- if [ "X$LIBCOPTIM" != "X" ]; then +- COPTIM=$COPTIM_save +- CFLAGS="${COPTIM} ${XCFLAGS}" +- fi +- cd ../.. + echo + echo "Returning to main configure." + echo +@@ -5094,53 +5059,6 @@ + echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" + ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} + echo +- echo "CCP4 configure: Running separate configure for libjwc_c library." +- echo +- cd ${srcdir}/${xwindir}/libjwc/libjwc_c +- echo "Updating modification times for configuration files in libjwc_c" +- echo "Please wait..." +- for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do +- touch $i && sleep 1 +- done +- echo "...done." +- echo +- echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" +- ( touch /tmp/$$.cache_file 2>/dev/null && \ +- cat /dev/null > /tmp/$$.cache_file && \ +- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ +- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} +- rm -f /tmp/$$.cache_file +- echo +- echo "CCP4 configure: Running separate configure for libjwc_f library." +- echo +- cd ${srcdir}/${xwindir}/libjwc/libjwc_f +- # for g77 3.1 some builds do not have no-common for system libs, +- # so disable for now +- echo "Updating modification times for configuration files in libjwc_f" +- echo "Please wait..." +- for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do +- touch $i && sleep 1 +- done +- echo "...done." +- echo +- # for g77 3.1 some builds do not have no-common for system libs, +- # so disable for now +- case $system in +- Darwin* ) +- echo "configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" +- ( touch /tmp/$$.cache_file 2>/dev/null && \ +- cat /dev/null > /tmp/$$.cache_file && \ +- ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ +- ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} +- ;; +- * ) +- echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" +- ( touch /tmp/$$.cache_file 2>/dev/null && \ +- cat /dev/null > /tmp/$$.cache_file && \ +- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ +- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} +- esac +- rm -f /tmp/$$.cache_file + + if test "$non_shared" = yes; then + #this is a bit of a cheat/fudge but that's life! +@@ -5210,12 +5128,6 @@ + fi + + echo +- echo "CCP4 configure: Running separate configure for Mosflm" +- echo +- cd ${srcdir}/${mosflmdir} +- echo "configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" +- ./configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} +- echo + cd ../.. + echo "Returning to main configure." + echo diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch new file mode 100644 index 000000000000..583697cea0a1 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch @@ -0,0 +1,87 @@ +--- ccp4-6.0.99e.orig/configure 2008-07-31 10:37:22.000000000 -0700 ++++ ccp4-6.0.99e/configure 2008-07-31 10:39:18.000000000 -0700 +@@ -643,45 +643,45 @@ + # echo "! Beware -- the $system installation isn't properly tested." ; } + syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' + +-if test -z "$onlylibs" ; then +- for i in CCP4_SCR BINSORT_SCR; do +- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the value of $i." +- badvar=1 +- fi +- done +- +- for i in libdir bindir includedir; do +- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the argument of --$i." +- badvar=1 +- fi +- done +- +- for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do +- if test -d $i || mkdir $i; then : +- else +- eval echo "! No directory $i and can\'t create it." +- badvar=1 +- fi +- done +-else +- # Kludge to fool the "Makefile" target in the top-level CCP4 +- # Makefile into not trying to remake src/Makefile.in +- for i in $srcdir/src $srcdir/lib/src ; do +- if test -d $i || mkdir $i; then +- if ! test -f $i/Makefile.in ; then +- echo +- echo "onlylibs: making dummy file $i/Makefile.in" +- touch $i/Makefile.in +- fi +- fi +- done +-fi ++#if test -z "$onlylibs" ; then ++# for i in CCP4_SCR BINSORT_SCR; do ++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the value of $i." ++# badvar=1 ++# fi ++# done ++# ++# for i in libdir bindir includedir; do ++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the argument of --$i." ++# badvar=1 ++# fi ++# done ++# ++# for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do ++# if test -d $i || mkdir $i; then : ++# else ++# eval echo "! No directory $i and can\'t create it." ++# badvar=1 ++# fi ++# done ++#else ++# # Kludge to fool the "Makefile" target in the top-level CCP4 ++# # Makefile into not trying to remake src/Makefile.in ++# for i in $srcdir/src $srcdir/lib/src ; do ++# if test -d $i || mkdir $i; then ++# if ! test -f $i/Makefile.in ; then ++# echo ++# echo "onlylibs: making dummy file $i/Makefile.in" ++# touch $i/Makefile.in ++# fi ++# fi ++# done ++#fi + + ### sanity checks + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-fix-setup-bash-incompatibility.patch b/sci-chemistry/ccp4-apps/files/6.1.3-fix-setup-bash-incompatibility.patch new file mode 100644 index 000000000000..d98f54cdb3c1 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-fix-setup-bash-incompatibility.patch @@ -0,0 +1,11 @@ +--- ccp4-6.0.99e.orig/include/ccp4.setup-bash 2008-07-31 10:37:22.000000000 -0700 ++++ ccp4-6.0.99e/include/ccp4.setup-bash 2008-07-31 12:47:14.000000000 -0700 +@@ -181,7 +181,7 @@ + + #Python path for the subprocess fixed module + +-if ($ccp4_first_in_path) then ++if [ $ccp4_first_in_path -eq 1 ]; then + setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} + else + setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch new file mode 100644 index 000000000000..9d8fefe965e5 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch @@ -0,0 +1,23 @@ +diff --git a/src/pisa/sbase/Makefile.am b/src/pisa/sbase/Makefile.am +index 053e83a..4ff3394 100755 +--- a/src/pisa/sbase/Makefile.am ++++ b/src/pisa/sbase/Makefile.am +@@ -1,4 +1,4 @@ +-pkgdatadir = $(datadir)/sbase ++pkgdatadir = $(datadir)/pisa/sbase + dist_pkgdata_DATA = \ + graph.sbase index.sbase struct.sbase + +diff --git a/src/pisa/sbase/Makefile.in b/src/pisa/sbase/Makefile.in +index faa3f7f..8630bd7 100755 +--- a/src/pisa/sbase/Makefile.in ++++ b/src/pisa/sbase/Makefile.in +@@ -62,7 +62,7 @@ POST_UNINSTALL = : + EXEEXT = @EXEEXT@ + OBJEXT = @OBJEXT@ + PATH_SEPARATOR = @PATH_SEPARATOR@ +-pkgdatadir = $(datadir)/sbase ++pkgdatadir = $(datadir)/pisa/sbase + AMTAR = @AMTAR@ + AR_FLAGS = @AR_FLAGS@ + AWK = @AWK@ diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch new file mode 100644 index 000000000000..7a012be6ef02 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch @@ -0,0 +1,65 @@ +diff --git a/ccp4-6.1.2/include/ccp4.setup-bash b/ccp4-6.1.2/include/ccp4.setup-bash +index 9848101..cea8ae6 100755 +--- a/ccp4-6.1.2/include/ccp4.setup-bash ++++ b/ccp4-6.1.2/include/ccp4.setup-bash +@@ -188,9 +188,9 @@ fi + #Python path for the subprocess fixed module + + if [ $ccp4_first_in_path -eq 1 ]; then +- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} ++ setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + else +- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python ++ setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + fi + + ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### +diff --git a/ccp4-6.1.2/include/ccp4.setup-csh b/ccp4-6.1.2/include/ccp4.setup-csh +index 42f0820..93c2cf3 100755 +--- a/ccp4-6.1.2/include/ccp4.setup-csh ++++ b/ccp4-6.1.2/include/ccp4.setup-csh +@@ -180,9 +180,9 @@ endif + #Python path for the subprocess fixed module + if (${?PYTHONPATH}) then + if ($ccp4_first_in_path) then +- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} ++ setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + else +- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python ++ setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + endif + else + setenv PYTHONPATH ${CCP4}/share/python +diff --git a/ccp4-6.1.2/include/ccp4.setup-sh b/ccp4-6.1.2/include/ccp4.setup-sh +index 4396ebf..a0455bd 100755 +--- a/ccp4-6.1.2/include/ccp4.setup-sh ++++ b/ccp4-6.1.2/include/ccp4.setup-sh +@@ -228,9 +228,9 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg + #Python path for the subprocess fixed module + + if test $ccp4_first_in_path -eq 1; then +- export PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} ++ export PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + else +- export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python ++ export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + fi + + ################### THE REST SHOULDN'T NEED EDITING ##################### +diff --git a/ccp4-6.1.2/include/ccp4.setup-zsh b/ccp4-6.1.2/include/ccp4.setup-zsh +index 0e5c2ce..53523f3 100755 +--- a/ccp4-6.1.2/include/ccp4.setup-zsh ++++ b/ccp4-6.1.2/include/ccp4.setup-zsh +@@ -157,10 +157,10 @@ export CLASSPATH + #Python path for the subprocess fixed module + + if ($ccp4_first_in_path) then +- PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} ++ PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + export PYTHONPATH + else +- PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python ++ PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + export PYTHONPATH + fi + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper.patch b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper.patch new file mode 100644 index 000000000000..a71c1354436c --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper.patch @@ -0,0 +1,77 @@ +--- src/rapper/LOOP/Makefile.in 2008-05-29 16:39:40.000000000 +0200 ++++ src/rapper/LOOP/Makefile.in.new 2009-03-12 20:40:03.157602172 +0100 +@@ -111,9 +111,9 @@ + pyexecdir = @pyexecdir@ + pythondir = @pythondir@ + rapper_LDFLAGS = @rapper_LDFLAGS@ +-bin_PROGRAMS = rapper ++bin_PROGRAMS = rappermc + +-rapper_SOURCES = \ ++rappermc_SOURCES = \ + kip.h aaconv.cpp atomconv.cpp kip_snake.cpp \ + kip_pdb.cpp measure.cpp lib_frags.cpp ran2.cpp \ + heap.cpp queue.cpp 3Dgeom.cpp space_grid.cpp list.cpp search_residue.cpp bitfield.cpp \ +@@ -129,7 +129,7 @@ + residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp + + +-rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la ++rappermc_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la + dist_pkgdata_DATA = params.xml + + INCLUDES = -I. -I../gc7.0/include -I../libxml2/include +@@ -139,7 +139,7 @@ + bin_PROGRAMS = rapper$(EXEEXT) + PROGRAMS = $(bin_PROGRAMS) + +-am_rapper_OBJECTS = aaconv.$(OBJEXT) atomconv.$(OBJEXT) \ ++am_rappermc_OBJECTS = aaconv.$(OBJEXT) atomconv.$(OBJEXT) \ + kip_snake.$(OBJEXT) kip_pdb.$(OBJEXT) measure.$(OBJEXT) \ + lib_frags.$(OBJEXT) ran2.$(OBJEXT) heap.$(OBJEXT) \ + queue.$(OBJEXT) 3Dgeom.$(OBJEXT) space_grid.$(OBJEXT) \ +@@ -164,8 +164,8 @@ + iterator.$(OBJEXT) residue_range.$(OBJEXT) \ + pop_search_frags.$(OBJEXT) saxs.$(OBJEXT) lib_choral.$(OBJEXT) \ + pdf.$(OBJEXT) WeightedDistribMean.$(OBJEXT) +-rapper_OBJECTS = $(am_rapper_OBJECTS) +-rapper_DEPENDENCIES = ../gc7.0/libgc.la ../libxml2/libxml2.la ++rappermc_OBJECTS = $(am_rapper_OBJECTS) ++rappermc_DEPENDENCIES = ../gc7.0/libgc.la ../libxml2/libxml2.la + + DEFS = @DEFS@ + DEFAULT_INCLUDES = -I. -I$(srcdir) +@@ -233,11 +233,11 @@ + CCLD = $(CC) + LINK = $(LIBTOOL) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ + $(AM_LDFLAGS) $(LDFLAGS) -o $@ +-DIST_SOURCES = $(rapper_SOURCES) ++DIST_SOURCES = $(rappermc_SOURCES) + DATA = $(dist_pkgdata_DATA) + + DIST_COMMON = $(dist_pkgdata_DATA) Makefile.am Makefile.in +-SOURCES = $(rapper_SOURCES) ++SOURCES = $(rappermc_SOURCES) + + all: all-am + +--- src/rapper/LOOP/Makefile.am 2008-01-24 15:08:17.000000000 +0100 ++++ src/rapper/LOOP/Makefile.am.new 2009-03-12 23:01:56.697533874 +0100 +@@ -1,6 +1,6 @@ +-bin_PROGRAMS = rapper ++bin_PROGRAMS = rappermc + +-rapper_SOURCES = \ ++rappermc_SOURCES = \ + kip.h aaconv.cpp atomconv.cpp kip_snake.cpp \ + kip_pdb.cpp measure.cpp lib_frags.cpp ran2.cpp \ + heap.cpp queue.cpp 3Dgeom.cpp space_grid.cpp list.cpp search_residue.cpp bitfield.cpp \ +@@ -15,7 +15,7 @@ + hash_table.cpp surface.cpp parse.cpp band.cpp edensity.cpp read_map.cpp iterator.cpp \ + residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp + +-rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la ++rappermc_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la + + pkgdatadir = $(datadir)/rapper + dist_pkgdata_DATA = params.xml diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-rename-truncate.patch b/sci-chemistry/ccp4-apps/files/6.1.3-rename-truncate.patch new file mode 100644 index 000000000000..43bfcf7c7a0e --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-rename-truncate.patch @@ -0,0 +1,42 @@ +coreutils now installs a binary called truncate. + +--- src/Makefile.in.orig 2009-03-02 23:25:45.000000000 -0800 ++++ src/Makefile.in 2009-03-02 23:25:53.000000000 -0800 +@@ -41,7 +41,7 @@ + professs r500 rantan rebatch reindex revise rfcorr rotamer rotmat \ + rstats rwcontents sapi scaleit scalepack2mtz seqwt sfall sigmaa sortmtz sortwater \ + stgrid stnet surface tffc tracer \ +-truncate unique vecref vectors volume watertidy watncs watpeak \ ++ftruncate unique vecref vectors volume watertidy watncs watpeak \ + wilson $(CIFTARGETS) + + BALBESTARGETS = search_DB get_structure_DB f2cif check_file_DB check_cell_sg \ +@@ -982,7 +982,7 @@ + surface: $(srcdir)/surface.f + tffc: $(srcdir)/tffc.f + tracer: $(srcdir)/tracer.f +-truncate: $(srcdir)/truncate.f ++ftruncate: $(srcdir)/truncate.f + unique: $(srcdir)/unique.f + vecref: $(srcdir)/vecref.f + vectors: $(srcdir)/vectors.f +--- examples/unix/runnable/truncate.exam.orig 2009-03-02 23:35:04.000000000 -0800 ++++ examples/unix/runnable/truncate.exam 2009-03-02 23:35:11.000000000 -0800 +@@ -15,7 +15,7 @@ + exit 1 + fi + # +-truncate hklin $CCP4_SCR/aucn_mrg.mtz \ ++ftruncate hklin $CCP4_SCR/aucn_mrg.mtz \ + hklout $CCP4_SCR/aucn_trn.mtz <<EOF-trunc + title DMSO red aucn2 Data - mosflm + truncate yes +@@ -28,7 +28,7 @@ + # do this if you already have Fs but want to look at the + # output graphs of TRUNCATE + +-truncate hklin $CEXAM/rnase/rnase18.mtz <<EOF ++ftruncate hklin $CEXAM/rnase/rnase18.mtz <<EOF + title Analysis of rnase data + labin F=FNAT SIGF=SIGFNAT + nresidue 192 diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-setup.patch b/sci-chemistry/ccp4-apps/files/6.1.3-setup.patch new file mode 100644 index 000000000000..c85c688debe4 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-setup.patch @@ -0,0 +1,336 @@ +diff --git a/include/ccp4.setup-bash b/include/ccp4.setup-bash +index 9848101..d76fe3b 100755 +--- a/include/ccp4.setup-bash ++++ b/include/ccp4.setup-bash +@@ -37,8 +37,8 @@ fi + # This is usually the directory in which you ran the tar command to unpack the + # code, and is assumed to be shared between machines at a multi-machine site. + +-setenv CCP4_MASTER /xtal +-setenv CCP4 $CCP4_MASTER/ccp4-6.1.2 ++setenv CCP4_MASTER /usr ++setenv CCP4 $CCP4_MASTER + + # Check for existence of CCP4_MASTER + if (! test -d $CCP4_MASTER) ; then +@@ -54,7 +54,7 @@ fi + # files. A dedicated scratch filesystem is probably better than (/usr)/tmp + # BINSORT_SCR: a scratch directory for binsort's use; normally same as CCP4_SCR + +-setenv CCP4_SCR /tmp/$USER ++setenv CCP4_SCR /tmp/$USER + # check to see if this exists and if not try to make it + test -d $CCP4_SCR || mkdir $CCP4_SCR + test -d $CCP4_SCR || \ +@@ -70,7 +70,7 @@ setenv CCP4I_TOP ${CCP4}/ccp4i + # For 'standard' installations this is /usr/local/bin + # but note the SGI distributed version of Tcl/Tk is not + # appropriate version +-setenv CCP4I_TCLTK /usr/local/bin ++setenv CCP4I_TCLTK /usr/bin + # CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help + setenv CCP4I_HELP ${CCP4I_TOP}/help + +@@ -128,7 +128,7 @@ setenv GFORTRAN_UNBUFFERED_ALL Y + # # for multiple systems + # foo) + setenv CBIN $CCP4/bin +- setenv CLIB $CCP4/lib ++ setenv CLIB $CCP4/GENTOOLIBDIR + + setenv CCP4_BROWSER firefox + +@@ -188,9 +188,9 @@ fi + #Python path for the subprocess fixed module + + if [ $ccp4_first_in_path -eq 1 ]; then +- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} ++ setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + else +- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python ++ setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + fi + + ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### +@@ -292,14 +292,12 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg + + ### dbCCP4i database handler setup ### + +-setenv DBCCP4I_TOP ${CCP4}/share/dbccp4i ++setenv DBCCP4I_TOP ${CCP4}/share/ccp4/dbccp4i + + ### IMOSFLM environment is now defined here + + setenv MOSFLM_EXEC ${CBIN}/ipmosflm + setenv MOSFLM_WISH ${CCP4I_TCLTK}/wish +-setenv IMOSFLM_VERSION "1.0.0" +- + + ### MMCIFDIC is now defined here. cif_mmdic.lib is a binary file === + # so on multiple installs it need to be unique and not in $CLIBD +@@ -309,21 +307,13 @@ setenv MMCIFDIC $CLIB/cif_mmdic.lib + ### MOLREPLIB Point to the location of the files bs-zeros.dat ps.resource symlib.blc + # They are distributed with CCP4 in $CLIBD. This env must have the trailing \ or / + +-setenv MOLREPLIB $CCP4/lib/data/monomers/ ++setenv MOLREPLIB $CCP4/share/ccp4/data/monomers/ + + ### CRANK points to location of Crank automation suite within ccp4i + +-setenv CRANK $CCP4/ccp4i/crank ++setenv CRANK $CCP4I_TOP/bin/crank + setenv CCP4_CRANK 1 + +-### XIA2 setup +-# XIAROOT directory (default is under the share folder) +- +-if test -e $CCP4/share/XIAROOT/setup.sh +-then +-. $CCP4/share/XIAROOT/setup.sh +-fi +- + # Note: The PATH is updated with the xia2 Applications directory in the + # construct below. + +@@ -339,7 +329,7 @@ fi + # They are distributed with CCP4 in $CLIBD/monomers. This env must have + # the trailing \ or / + +-setenv CLIBD_MON $CCP4/lib/data/monomers/ ++setenv CLIBD_MON $CCP4/share/ccp4/data/monomers/ + + ### PUBLIC_FONT84, CCP4_HELPDIR, HELPDIR, MOSHELPFILE ### + # (essential for the relevant programs) +@@ -347,10 +337,10 @@ setenv PUBLIC_FONT84 $CLIB/font84.dat # plot84 fonts [used by plot84lib] + + # location of VMS-style help files required for mosflm [used by hlplib, chelp, + # chlp, (ip)mosflm]: +-setenv CCP4_HELPDIR $CCP4/help/ # NB trailing / ++setenv CCP4_HELPDIR $CCP4I_TOP/help/ # NB trailing / + + # Rasmol path. Needed for prog. to find rasmol.hlp +-setenv RASMOLPATH $CCP4/x-windows/RasMol/src ++setenv RASMOLPATH $CCP4/GENTOOLIBDIR/rasmol + + # CCP4 executables and scripts live in $CBIN and $CETC respectively; put them + # on the path in an appropriate order for scripts to be used as wrappers for +@@ -373,32 +363,14 @@ done + + # Optional (useful) additional environment variables + setenv CCP4 $CCP4 +- setenv CDOC $CCP4/doc +- setenv CHTML $CCP4/html +- setenv CETC $CCP4/etc +- setenv CEXAM $CCP4/examples ++ setenv CDOC $DBCCP4I_TOP/doc ++ setenv CHTML $CCP4I_TOP/html ++ setenv CETC $CCP4I_TOP/etc ++ setenv CEXAM $CLIB/ccp4/examples + setenv CINCL $CCP4/include +- setenv CLIBD $CCP4/lib/data +- setenv CLIBS $CCP4/lib/src +- setenv CPROG $CCP4/src ++ setenv CLIBD $CCP4/share/ccp4/data + + if [ "`basename $SHELL`" != "ksh" ]; then +-# useful aliases, at least for developers +- alias ccp4 'pushd $CCP4>/dev/null' +- alias xtal 'pushd $CCP4_MASTER>/dev/null' +- alias cbin 'pushd $CBIN>/dev/null' +- alias cetc 'pushd $CETC>/dev/null' +- alias cprog 'pushd $CPROG>/dev/null' +- alias cincl 'pushd $CINCL>/dev/null' +- alias clib 'pushd $CLIB>/dev/null' +- alias clibd 'pushd $CLIBD>/dev/null' +- alias clibs 'pushd $CLIBS>/dev/null' +- alias cbin 'pushd $CBIN>/dev/null' +- alias cexam 'pushd $CEXAM>/dev/null' +- alias cdoc 'pushd $CDOC>/dev/null' +- alias chtml 'pushd $CHTML>/dev/null' +- alias ccp4help '$CCP4_BROWSER $CHTML/INDEX.html \&' +- + ### laue, lget, linkimages ### + + ### only if we have the Laue software suite... +@@ -430,23 +402,6 @@ if [ "`basename $SHELL`" != "ksh" ]; then + alias lbin 'pushd $CBIN>/dev/null' + + fi +- ++else + unset alias # clean up + fi # ksh test +- +-# Set-up cctbx environment +-test -r $CCP4/lib/cctbx/cctbx_build/setpaths.sh && . $CCP4/lib/cctbx/cctbx_build/setpaths.sh +- +-# Set-up phaser environment +-if ( test -d $CCP4/src/phaser) ; then +- phaser_mtype=`$CCP4/src/phaser/bin/machine_type` +- phaser_version=`grep PHASER_VERSION $CCP4/src/phaser/conf/version.sh | awk '{print $3}'` +- phaser_setup_file="${CCP4}/src/phaser/phaser-${phaser_version}/build/${phaser_mtype}/setpaths.sh" +- test -r $phaser_setup_file && . $phaser_setup_file +-fi +- +-#BALBES root configuration +-if ( test -d $CCP4/share/balbes/BALBES_0.0.1) +-then +- setenv BALBES_ROOT $CCP4/share/balbes/BALBES_0.0.1 +-fi +diff --git a/include/ccp4.setup-csh b/include/ccp4.setup-csh +index 42f0820..ed3c671 100755 +--- a/include/ccp4.setup-csh ++++ b/include/ccp4.setup-csh +@@ -24,8 +24,8 @@ + # This is usually the directory in which you ran the tar command to unpack the + # code, and is assumed to be shared between machines at a multi-machine site. + +-setenv CCP4_MASTER /xtal +-setenv CCP4 $CCP4_MASTER/ccp4-6.1.2 ++setenv CCP4_MASTER /usr ++setenv CCP4 $CCP4_MASTER + + # Check for existence of CCP4_MASTER + if (! -e $CCP4_MASTER) then +@@ -57,7 +57,7 @@ setenv CCP4I_TOP ${CCP4}/ccp4i + # For 'standard' installations this is /usr/local/bin + # but note the SGI distributed version of Tcl/Tk is not + # appropriate version +-setenv CCP4I_TCLTK /usr/local/bin ++setenv CCP4I_TCLTK /usr/bin + # CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help + setenv CCP4I_HELP ${CCP4I_TOP}/help + +@@ -115,7 +115,7 @@ setenv GFORTRAN_UNBUFFERED_ALL Y + # # for multiple systems + # case 'foo': + setenv CBIN $CCP4/bin +- setenv CLIB $CCP4/lib ++ setenv CLIB $CCP4/GENTOOLIBDIR + + setenv CCP4_BROWSER firefox + +@@ -180,9 +180,9 @@ endif + #Python path for the subprocess fixed module + if (${?PYTHONPATH}) then + if ($ccp4_first_in_path) then +- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} ++ setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + else +- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python ++ setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + endif + else + setenv PYTHONPATH ${CCP4}/share/python +@@ -284,13 +284,12 @@ if (-e $CCP4/include/ccp4.msg) cat $CCP4/include/ccp4.msg + + ### dbCCP4i database handler setup ### + +-setenv DBCCP4I_TOP ${CCP4}/share/dbccp4i ++setenv DBCCP4I_TOP ${CCP4}/share/ccp4/dbccp4i + + ### IMOSFLM environment is now defined here + + setenv MOSFLM_EXEC ${CBIN}/ipmosflm + setenv MOSFLM_WISH ${CCP4I_TCLTK}/wish +-setenv IMOSFLM_VERSION "1.0.0" + + ### MMCIFDIC is now defined here. cif_mmdic.lib is a binary file === + # so on multiple installs it need to be unique and not in $CLIBD +@@ -300,20 +299,13 @@ setenv MMCIFDIC $CLIB/cif_mmdic.lib + ### MOLREPLIB Point to the location of the files bs-zeros.dat ps.resource symlib.blc + # They are distributed with CCP4 in $CLIBD. This env must have the trailing \ or / + +-setenv MOLREPLIB $CCP4/lib/data/monomers/ ++setenv MOLREPLIB $CCP4/share/ccp4/data/monomers/ + + ### CRANK points to location of Crank automation suite within ccp4i + +-setenv CRANK $CCP4/ccp4i/crank ++setenv CRANK $CCP4I_TOP/bin/crank + setenv CCP4_CRANK 1 + +-### XIA2 setup +-# XIAROOT directory (default is under the share folder) +- +-if (-e $CCP4/share/XIAROOT/setup.csh) then +- source $CCP4/share/XIAROOT/setup.csh +-endif +- + # Note: The PATH is updated with the xia2 Applications directory in the + # construct below. + +@@ -328,7 +320,7 @@ endif + # They are distributed with CCP4 in $CLIBD/monomers. This env must have + # the trailing \ or / + +-setenv CLIBD_MON $CCP4/lib/data/monomers/ ++setenv CLIBD_MON $CCP4/share/ccp4/data/monomers/ + + ### PUBLIC_FONT84, CCP4_HELPDIR, HELPDIR, MOSHELPFILE ### + # (essential for the relevant programs) +@@ -339,7 +331,7 @@ setenv PUBLIC_FONT84 $CLIB/font84.dat # plot84 fonts [used by plot84lib] + setenv CCP4_HELPDIR $CCP4/help/ # NB trailing / + + # Rasmol path. Needed for prog. to find rasmol.hlp +-setenv RASMOLPATH $CCP4/x-windows/RasMol/src ++setenv RASMOLPATH $CCP4/GENTOOLIBDIR/rasmol + + # CCP4 executables and scripts live in $CBIN and $CETC respectively; put them + # on the path in an appropriate order for scripts to be used as wrappers for +@@ -366,30 +358,12 @@ end + + # Optional (useful) additional environment variables + setenv CCP4 $CCP4 +- setenv CDOC $CCP4/doc +- setenv CHTML $CCP4/html +- setenv CETC $CCP4/etc +- setenv CEXAM $CCP4/examples ++ setenv CDOC $DBCCP4I_TOP/doc ++ setenv CHTML $CCP4I_TOP/html ++ setenv CETC $CCP4I_TOP/etc ++ setenv CEXAM $CLIB/ccp4/examples + setenv CINCL $CCP4/include +- setenv CLIBD $CCP4/lib/data +- setenv CLIBS $CCP4/lib/src +- setenv CPROG $CCP4/src +- +-# useful aliases, at least for developers +- alias ccp4 'pushd $CCP4>/dev/null' +- alias xtal 'pushd $CCP4_MASTER>/dev/null' +- alias cbin 'pushd $CBIN>/dev/null' +- alias cetc 'pushd $CETC>/dev/null' +- alias cprog 'pushd $CPROG>/dev/null' +- alias cincl 'pushd $CINCL>/dev/null' +- alias clib 'pushd $CLIB>/dev/null' +- alias clibd 'pushd $CLIBD>/dev/null' +- alias clibs 'pushd $CLIBS>/dev/null' +- alias cbin 'pushd $CBIN>/dev/null' +- alias cexam 'pushd $CEXAM>/dev/null' +- alias cdoc 'pushd $CDOC>/dev/null' +- alias chtml 'pushd $CHTML>/dev/null' +- alias ccp4help '$CCP4_BROWSER $CHTML/INDEX.html &' ++ setenv CLIBD $CCP4/share/ccp4/data + + ### laue, lget, linkimages ### + +@@ -421,19 +395,3 @@ end + # + + endif +- +-# Set-up cctbx environment +-if (-e $CCP4/lib/cctbx/cctbx_build/setpaths.csh) source $CCP4/lib/cctbx/cctbx_build/setpaths.csh +- +-# Set-up phaser environment +-if (-d $CCP4/src/phaser) then +- set phaser_mtype = `$CCP4/src/phaser/bin/machine_type` +- set phaser_version = `grep PHASER_VERSION $CCP4/src/phaser/conf/version.csh | awk '{print $3}'` +- set phaser_setup_file = "${CCP4}/src/phaser/phaser-${phaser_version}/build/${phaser_mtype}/setpaths.csh" +- if (-e $phaser_setup_file) source $phaser_setup_file +-endif +- +-#BALBES root configuration +-if ( -d $CCP4/share/balbes/BALBES_0.0.1) then +- setenv BALBES_ROOT $CCP4/share/balbes/BALBES_0.0.1 +-endif diff --git a/sci-chemistry/ccp4-apps/metadata.xml b/sci-chemistry/ccp4-apps/metadata.xml new file mode 100644 index 000000000000..9ac9ffdb3a41 --- /dev/null +++ b/sci-chemistry/ccp4-apps/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-chemistry</herd> +</pkgmetadata> |