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authorJustin Lecher <jlec@gentoo.org>2010-02-06 00:37:43 +0000
committerJustin Lecher <jlec@gentoo.org>2010-02-06 00:37:43 +0000
commit571e1f99857556e2876532f37882336f5bd72be1 (patch)
treeecee8dc95498811153f952164fd0c05a2ea55551 /sci-chemistry/ccp4-apps
parentAutomated update of use.local.desc (diff)
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splitted apps from ccp4
(Portage version: 2.2_rc62/cvs/Linux x86_64)
Diffstat (limited to 'sci-chemistry/ccp4-apps')
-rw-r--r--sci-chemistry/ccp4-apps/ChangeLog20
-rw-r--r--sci-chemistry/ccp4-apps/ccp4-apps-6.1.3.ebuild431
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-clipper-mmdbold-ggc-4.3.patch22
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch70
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch24
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch11
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch35
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch19
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch42
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch14
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch111
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch87
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-fix-setup-bash-incompatibility.patch11
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch23
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch65
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper.patch77
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-rename-truncate.patch42
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-setup.patch336
-rw-r--r--sci-chemistry/ccp4-apps/metadata.xml5
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>