Streamline configure

Package-Manager: portage-2.2.0_alpha26/cvs/Linux x86_64

10 files changed, 468 insertions, 523 deletions

diff --git a/sci-chemistry/ccp4-apps/ChangeLog b/sci-chemistry/ccp4-apps/ChangeLog
index cee6b417d362..b72b6eac9251 100644
--- a/sci-chemistry/ccp4-apps/ChangeLog
+++ b/sci-chemistry/ccp4-apps/ChangeLog
@@ -1,6 +1,17 @@
 # ChangeLog for sci-chemistry/ccp4-apps
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.23 2011/03/02 17:53:22 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.24 2011/03/04 17:02:15 jlec Exp $
+
+*ccp4-apps-6.1.3-r9 (04 Mar 2011)
+
+  04 Mar 2011; Justin Lecher <jlec@gentoo.org>
+  -files/6.1.3-clipper-mmdbold-ggc-4.3.patch,
+  +files/6.1.3-rename-rapper-ng.patch,
+  -files/6.1.3-fix-setup-bash-incompatibility.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-r8.ebuild,
+  +ccp4-apps-6.1.3-r9.ebuild:
+  Streamline configure
 
   02 Mar 2011; Justin Lecher <jlec@gentoo.org> ccp4-apps-6.1.3-r7.ebuild,
   ccp4-apps-6.1.3-r8.ebuild:
diff --git a/sci-chemistry/ccp4-apps/Manifest b/sci-chemistry/ccp4-apps/Manifest
index ab8c2a469a7d..68ced63718c3 100644
--- a/sci-chemistry/ccp4-apps/Manifest
+++ b/sci-chemistry/ccp4-apps/Manifest
@@ -1,7 +1,6 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA1
 
-AUX 6.1.3-clipper-mmdbold-ggc-4.3.patch 656 RMD160 6b302779b48217a14f5ac9110bc307db3a3b51eb SHA1 f5813d6769fa9dc11605425cdbda85691d3016bc SHA256 982eff0336a6dfaf4e280d51a59cf722fc063ca89d15ca0af46ce83727fb9a8a
 AUX 6.1.3-clipper-template.patch 2619 RMD160 a3a4998365c4e516325cf95472e8493729ee4b46 SHA1 f3d92469ac5ec4483818abbf50c32ac9b05a622c SHA256 a185a93f76c23ce06256866cfaf0e9854a5702b95a1e49e4d3a5f732e0d1e2a3
 AUX 6.1.3-dont-build-balbes.patch 489 RMD160 7ee9ad48afcd6dd261277321be681bb41ce73fbb SHA1 56f045d3ec8dbf4e0c83dc9df2ac478bd4c5268c SHA256 dfe1b810fb07bf536528b9c955e3162dc470a803513ae6fa69848ed6d64503c4
 AUX 6.1.3-dont-build-double-and-make-bindir.patch 688 RMD160 f5f93cbec122ce81a1ddb1cf57a852d51fa5e5d6 SHA1 4c924554c5c1991ed691fe3474eeffbd108493a9 SHA256 037a3d9042c784c895083fe5348ed3bde74620c1b6b3b2cd4eea53bdbfe77d53
@@ -12,23 +11,21 @@ AUX 6.1.3-dont-build-scala.patch 2185 RMD160 52b3e962b534664a104fbc74ee4d6bad250
 AUX 6.1.3-dont-build-xia.patch 712 RMD160 dd3f8bcf309b7d84c31bf4cf829d1d9f95618d4a SHA1 b4e32e245bd8f5fde6a9573777592b3787f5becd SHA256 931bf9027e503d19d1d4446ea3ada2c20044b355d8071756ae58e88159eab75f
 AUX 6.1.3-dont-configure.patch 4592 RMD160 301eeb912704ff01ab7e324e951c2d5770739f88 SHA1 66e61f7d2979cfd6d304238ae665d4e114368279 SHA256 817e37a623a74cc06017c5cd7b10fc5afb75242a519820825610c09ad4c91741
 AUX 6.1.3-dont-make-dirs-in-configure.patch 2866 RMD160 ba49e45ab609a42a2d93b96f55af913bf9625610 SHA1 36c9329c3768c08687ef062c9ab649d32833b422 SHA256 1b5997f17526a4fd60ffa9eccf4b765aadf3a78c9394657000e0454f364240ca
-AUX 6.1.3-fix-setup-bash-incompatibility.patch 422 RMD160 e7e886ab030cf3324302c8fd0c866b48eeb34f8c SHA1 4e549abcd3ced1e6ecf9d3f2bddfed70425d61aa SHA256 109a0e806f9c0e1b8bf5e5f0c58be6f1dae06396b62ee4dae9f579ff7dcb5a01
 AUX 6.1.3-impl-dec.patch 4302 RMD160 2b69341db71699504e4444d18db7db1d4fc10ddd SHA1 b3a9b71355063fbe34b0d3db4163d7e3689cb0a1 SHA256 73c3137ab8e20c25d1dfcfc65011a055f90eb902eede697c7dfbc5f37948eb18
 AUX 6.1.3-pisa.patch 714 RMD160 9923901ec82dc0c7cd2a13f1eb6362a11576abd8 SHA1 8d7e0b730b9969d2d59a6b9441b7c3709b397e16 SHA256 42a581d2a9747239c1b129dbeffc76a2532de320629dd58112a42ffde669bf12
 AUX 6.1.3-pythonpath.patch 2716 RMD160 f46963e6c4c48cfab76062aaff8d58189f9d590b SHA1 24f6c9a051f97d9e5db5c4fb9ef457114fa7a951 SHA256 41ca8ed3fc1701caa18b30f44af7475d49fc0042ee058bae3d8c8617a6d9bcc2
-AUX 6.1.3-rename-rapper.patch 2856 RMD160 37504bed3cb4e1858d88331305deef6564616b02 SHA1 31f513c987e1408b868f8c9de4aaa9f2c35cb378 SHA256 d9fed1ec65089c4130358aeed771b32c1253e48a73e90f0ce7b92bd0abbb0c2b
-AUX 6.1.3-rename-truncate.patch 1515 RMD160 eff332faa67a1732e0f99cc6cdcb846932eadc87 SHA1 b504542cf710e1b54a684b0fa0e8d73d967c96ac SHA256 50a59a1856867daa3de1f8f53e92bcfe74dea3a6d3c4ba238a9ea83dbcdfbf07
-AUX 6.1.3-setup.patch 12338 RMD160 2107d599dfe477863710d6b8098b3ca43b8cd22d SHA1 38b3d6ef1e40bf505f4227646d9afce1fe828395 SHA256 c9843cf27af9809ecf96a700521972aa434970a7fdaaf571c36b05fd4be516eb
+AUX 6.1.3-rename-rapper-ng.patch 2241 RMD160 63cda7686f10316f2a9d0a12346de9d41c95d6cc SHA1 a08d3176e8939619893d1007685dda9be5fc78be SHA256 7a476133860463b91b39189aa5628607f0404224cae1273b4da1c500a845dfdb
 DIST 6.1.3-oasis4.0.patch.bz2 946 RMD160 b448376114ba41e6999d533929fdb79812476f87 SHA1 7667aca14d28cec01bfa7d2eee9cbce11624f4fa SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b
 DIST ccp4-6.1.3-core-src.tar.gz 242134076 RMD160 e9b7deb0766fb95d5e8946881f20e086f0896fe9 SHA1 ee5ada892694db5dc9b2d7d2330b4ac694f56580 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324
 EBUILD ccp4-apps-6.1.3-r7.ebuild 10229 RMD160 8506cfc52e0170b54269db2bc44e92f159d3ede9 SHA1 c19f6805be68dd87d037a0f34b7aeb3a986e4825 SHA256 2b4202fd0b27ec592641738d09b3ec76da068452eb4b101502b171c826aa3ca1
-EBUILD ccp4-apps-6.1.3-r8.ebuild 10659 RMD160 ba65e688bb42fecd33436175e91529957967b66d SHA1 21bd898623e6ee2be672c0b491b4bb6903a6dc5e SHA256 98c69cb797d62643a704474b1d7acc711744a38e9b0aeda21d5b235a64daa5d8
-MISC ChangeLog 4256 RMD160 cf9d5e6c526bb771c97c548a664c718c69f6e847 SHA1 abe7a1221dd350c085e410d921c6b43fe99a5add SHA256 238f4169d31de17e942f79fb9a07c85de9e69237c116fe2deaa0f58508f97b2d
+EBUILD ccp4-apps-6.1.3-r8.ebuild 9955 RMD160 b280024cd8d730442333d57e1e73ac45aa72e2a0 SHA1 3bd5bfc3cae357effcec71dfca0d4d761654f899 SHA256 fa5e1e42669e018f751ac5bf18172b32d47f7b13b580d042f0eb8e3d9b22f2a7
+EBUILD ccp4-apps-6.1.3-r9.ebuild 9955 RMD160 bec770db85c26e1eebdcb94a94382206baf9aafe SHA1 ca9633cc1188a292c589553625928ff076f4be1e SHA256 5567759793e7c583166abc778ebd57e15cc49c100e544f47f012248a37c7b5f5
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diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r8.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r8.ebuild
index 6f2ca5492d16..0bef8dc77473 100644
--- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r8.ebuild
+++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r8.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r8.ebuild,v 1.3 2011/03/02 17:53:22 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r8.ebuild,v 1.4 2011/03/04 17:02:15 jlec Exp $
 
 EAPI="3"
 
@@ -133,16 +133,6 @@ src_prepare() {
 	# libraries come from sci-libs/ccp4-libs
 	ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch
 
-	# coreutils installs a binary called truncate
-#	ccp_patch "${FILESDIR}"/${PV}-rename-truncate.patch
-#	mv ./doc/truncate.doc ./doc/ftruncate.doc || die
-#	mv ./html/truncate.html ./html/ftruncate.html || die
-
-	# conflicts with media-libs/raptor
-#	ccp_patch "${FILESDIR}"/${PV}-rename-rapper.patch
-#	mv ./doc/rapper.doc ./doc/rappermc.doc || die
-#	mv ./html/rapper.html ./html/rappermc.html || die
-
 	# We have seperate ebuilds for those
 	for bin in molref xia scala imosflm balbes; do
 		ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch
@@ -163,6 +153,9 @@ src_prepare() {
 	# Fix upstreams code
 	ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
 
+	# Not renaming, but unbundling libs
+	ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch
+
 	# Update things for oasis 4 usage
 	epatch "${WORKDIR}"/${PV}-oasis4.0.patch
 	sed 's: oasis : :g' -i src/Makefile.in || die
@@ -186,19 +179,7 @@ src_prepare() {
 
 	# 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 '/^rapper_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${EPREFIX}/usr/include/gc -I${EPREFIX}/usr/include/libxml2:g" \
-		LOOP/Makefile.am
-	eautoreconf
+		eautoreconf
 	popd 2>/dev/null
 
 	gnuconfig_update
diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r9.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r9.ebuild
new file mode 100644
index 000000000000..bf22bc2e8b95
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r9.ebuild
@@ -0,0 +1,384 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r9.ebuild,v 1.1 2011/03/04 17:02:15 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+
+inherit autotools eutils flag-o-matic gnuconfig python toolchain-funcs
+
+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/${!NAME}"
+done
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples X"
+
+X11DEPS="
+	x11-libs/libX11
+	x11-libs/libXaw
+	x11-libs/libXt
+	x11-libs/libxdl_view"
+
+TKDEPS="
+	>=dev-lang/tk-8.3
+	>=dev-tcltk/blt-2.4
+	dev-tcltk/iwidgets
+	dev-tcltk/itcl
+	dev-tcltk/itk
+	>=dev-tcltk/tdom-0.8
+	dev-tcltk/tkimg
+	dev-tcltk/tktreectrl"
+
+SCILIBS="
+	~sci-libs/ccp4-libs-${PV}
+	>=sci-libs/ccp4-libs-${PV}-r7
+	sci-libs/clipper
+	sci-libs/fftw:2.1
+	sci-libs/mmdb
+	virtual/blas
+	virtual/lapack"
+
+SCIAPPS="
+	sci-chemistry/pdb-extract
+	sci-chemistry/pymol
+	sci-chemistry/rasmol
+	>=sci-chemistry/oasis-4.0-r1"
+
+RDEPEND="
+	${TKDEPS}
+	${SCILIBS}
+	app-shells/tcsh
+	dev-python/pyxml
+	dev-libs/libxml2:2
+	dev-libs/libjwc_c
+	dev-libs/libjwc_f
+	dev-libs/boehm-gc
+	!app-office/sc
+	!<sci-chemistry/ccp4-6.1.3
+	X? ( ${X11DEPS} )"
+DEPEND="${RDEPEND}
+	X? (
+		x11-misc/imake
+		x11-proto/inputproto
+		x11-proto/xextproto
+	)"
+PDEPEND="${SCIAPPS}"
+
+S="${WORKDIR}/${MY_P}"
+
+pkg_setup() {
+	python_set_active_version 2
+}
+
+src_prepare() {
+	einfo "Applying upstream patches ..."
+	for patch in $(seq $PATCH_TOT); do
+		base="PATCH${patch}"
+		dir=$(eval echo \${${base}[0]})
+		p=$(eval echo \${${base}[1]})
+		pushd "${dir}" >& /dev/null
+		ccp_patch "${DISTDIR}/${p}"
+		popd >& /dev/null
+	done
+	einfo "Done."
+	echo
+
+	[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
+
+	einfo "Applying Gentoo patches ..."
+
+	# it tries to create libdir, bindir etc on live system in configure
+	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
+
+	# We already have sci-chemistry/rasmol
+	# Also remember to create the bindir.
+	ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch
+
+	# libraries come from sci-libs/ccp4-libs
+	ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch
+
+	# We have seperate ebuilds for those
+	for bin in molref xia scala imosflm balbes; do
+		ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch
+	done
+
+	# don't configure what is not build
+	ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch
+
+	# Set python paths correctly
+	ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch
+
+	# Set python paths correctly
+	ccp_patch "${FILESDIR}"/${PV}-pisa.patch
+
+	# Set python paths correctly
+	ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch
+
+	# Fix upstreams code
+	ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
+
+	# Not renaming, but unbundling libs
+	ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch
+
+	# Update things for oasis 4 usage
+	epatch "${WORKDIR}"/${PV}-oasis4.0.patch
+	sed 's: oasis : :g' -i src/Makefile.in || die
+
+	einfo "Done." # done applying Gentoo patches
+	echo
+
+	sed \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		-e 's:-Wl,-rpath,$CLIB::g' \
+		-e 's: -rpath $CLIB::g' \
+		-e 's: -I${srcdir}/include/cpp_c_headers::g' \
+		-e 's:sleep 1:sleep .2:g' \
+		-i configure || die
+
+	find "${S}" -name "Makefile.*" \
+		-exec sed -e 's|_FLAGS-|_FLAGS:-|g' -e "s:\(eval \$([[:alnum:]]*)\):\1 \$(GENTOOLDFLAGS):g" -i '{}' \;
+
+	# Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version
+	sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure
+
+	# Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
+	pushd src/rapper 2>/dev/null
+		eautoreconf
+	popd 2>/dev/null
+
+	gnuconfig_update
+
+	python_convert_shebangs $(python_get_version) src/ccp4_pipeline_simple.py ./share/smartie/*.py
+}
+
+src_configure() {
+	# Build system is broken if we set LDFLAGS
+	export GENTOOLDFLAGS="${LDFLAGS}"
+	unset LDFLAGS
+
+	# These are broken with ./src/procheck/ps.f
+	filter-flags "-floop-*"
+
+	# GENTOO_OSNAME can be one of:
+	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
+	# linux_compaq_compilers linux_intel_compilers generic Darwin
+	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
+	if [[ "$(tc-getFC)" = "ifort" ]]; then
+		if use ia64; then
+			GENTOO_OSNAME="ia64_linux_intel"
+		else
+			# Should be valid for x86, maybe amd64
+			GENTOO_OSNAME="linux_intel_compilers"
+		fi
+	else
+		# Should be valid for x86 and amd64, at least
+		GENTOO_OSNAME="linux"
+	fi
+
+	# Sets up env
+	ln -s \
+		ccp4.setup-bash \
+		"${S}"/include/ccp4.setup
+
+	# We agree to the license by emerging this, set in LICENSE
+	sed -i \
+		-e "s~^\(^agreed=\).*~\1yes~g" \
+		"${S}"/configure
+
+	# Fix up variables -- need to reset CCP4_MASTER at install-time
+	sed -i \
+		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
+		-e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
+		-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
+		-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
+		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
+		"${S}"/include/ccp4.setup*
+
+	# Set up variables for build
+	source "${S}"/include/ccp4.setup-sh
+
+	export CC=$(tc-getCC)
+	export CXX=$(tc-getCXX)
+	export COPTIM=${CFLAGS}
+	export CXXOPTIM=${CXXFLAGS}
+	# Default to -O2 if FFLAGS is unset
+	export FC=$(tc-getFC)
+	export FOPTIM=${FFLAGS:- -O2}
+	export BINSORT_SCR="${T}"
+	export CCP4_MASTER="${WORKDIR}"
+	export CCP4I_TCLTK="${EPREFIX}/usr/bin"
+	export MAKE="make ${MAKEOPTS} ${EXTRA_EMAKE}"
+
+	# Can't use econf, configure rejects unknown options like --prefix
+	./configure \
+		$(use_enable X x) \
+		--with-shared-libs \
+		--with-fftw="${EPREFIX}/usr" \
+		--with-warnings \
+		--disable-pdb_extract \
+		--disable-cctbx \
+		--disable-phaser \
+		--disable-diffractionImg \
+		--disable-clipper \
+		--disable-mosflm \
+		--disable-mrbump \
+		--tmpdir="${TMPDIR}" \
+		${GENTOO_OSNAME} || die "econf failed"
+
+	# We do this manually, since disabling the clipper libraries also
+	# disables the clipper programs
+	pushd src/clipper_progs 2>/dev/null
+	econf \
+		--prefix="${S}" \
+		--bindir="${ED}"/usr/libexec/ccp4/bin \
+		--with-ccp4="${S}" \
+		--with-clipper="${EPREFIX}/usr" \
+		--with-fftw="${EPREFIX}/usr" \
+		--with-mmdb="${EPREFIX}/usr" \
+		CXX=$(tc-getCXX)
+	popd 2>/dev/null
+}
+
+src_compile() {
+	# fsplit is required for the programs
+	pushd lib/src 2>/dev/null
+		emake fsplit -j1 || die
+	popd 2>/dev/null
+
+	# We do this manually, since disabling the clipper libraries also
+	# disables the clipper programs
+	pushd src/clipper_progs 2>/dev/null
+		emake || die
+	popd 2>/dev/null
+
+	emake -j1 || die "emake failed"
+}
+
+src_install() {
+	# Set up variables for build
+	source "${S}"/include/ccp4.setup-sh
+
+	# if we don't make this, a ton of programs fail to install
+	mkdir "${S}"/bin || die
+
+	# We do this manually, since disabling the clipper libraries also
+	# disables the clipper programs
+	pushd "${S}"/src/clipper_progs 2>/dev/null
+		emake install || die
+	popd 2>/dev/null
+
+	einstall || die "install failed"
+
+	# Collision with sci-chemistry/mrbump
+	rm -f "${S}"/bin/{mrbump,pydbviewer} || die
+
+	# Bins
+	exeinto /usr/libexec/ccp4/bin/
+	doexe "${S}"/bin/* || die
+
+	# Libs
+	for file in "${S}"/lib/*; do
+		if [[ -d ${file} ]]; then
+			continue
+		elif [[ -x ${file} ]]; then
+			dolib.so ${file} || die
+		else
+			insinto /usr/$(get_libdir)
+			doins ${file} || die
+		fi
+	done
+
+	rm -f "${S}"/include/ccp4.setup*
+
+	# smartie -- log parsing
+	insinto /usr/share/ccp4
+	doins -r "${S}"/share/smartie || die
+
+	# Install docs and examples
+	doman "${S}"/man/cat1/*
+
+	mv "${S}"/manual/README "${S}"/manual/README-manual
+	dodoc manual/* README CHANGES doc/* examples/README || die
+
+	rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.*
+	rm "${ED}"/usr/share/doc/${PF}/COPYING.*
+
+	dohtml -r "${S}"/html/*
+
+	if use examples; then
+		for i in data rnase toxd; do
+			docinto examples/${i}
+			dodoc "${S}"/examples/${i}/*
+		done
+
+		docinto examples/tutorial
+		dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css
+		for i in data results; do
+			docinto examples/tutorial/${i}
+			dodoc "${S}"/examples/tutorial/${i}/*
+		done
+
+		for i in non-runnable runnable; do
+			docinto examples/unix/${i}
+			dodoc "${S}"/examples/unix/${i}/*
+		done
+	fi
+	# Needed for ccp4i docs to work
+	dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die
+	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die
+
+	# Fix overlaps with other packages
+	rm -f "${ED}"/usr/share/man/man1/rasmol.1* "${ED}"/usr/lib/font84.dat || die
+	mv "${ED}"/usr/share/man/man1/truncate{,-ccp4}.1 || die
+	mv "${ED}"/usr/share/man/man1/rapper{,-ccp4}.1 || die
+	mv "${ED}"/usr/share/man/man1/sc{,-ccp4}.1 || die
+
+	cat >> "${T}"/baubles <<- EOF
+	#!${EPREFIX}/bin/bash
+	exec $(PYTHON) \${CCP4}/share/ccp4/smartie/baubles.py
+	EOF
+
+	exeinto /usr/libexec/ccp4/bin/
+	doexe "${T}"/baubles || die
+}
+
+# Epatch wrapper for bulk patching
+ccp_patch() {
+	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
+}
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-mmdbold-ggc-4.3.patch b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-mmdbold-ggc-4.3.patch
deleted file mode 100644
index 66186609a668..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-mmdbold-ggc-4.3.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- ccp4-6.0.99e.orig/lib/clipper/clipper/mmdbold/clipper_mmdb.cpp	2008-07-31 13:23:13.000000000 -0700
-+++ ccp4-6.0.99e/lib/clipper/clipper/mmdbold/clipper_mmdb.cpp	2008-07-31 13:47:35.000000000 -0700
-@@ -43,7 +43,7 @@
- 
- #include <set>
- #include <algorithm>
--
-+#include <string.h>
- 
- namespace clipper {
- 
---- ccp4-6.0.99e.orig/lib/clipper/clipper/mmdbold/clipper_mmdb_wrapper.cpp.orig	2008-07-31 13:49:53.000000000 -0700
-+++ ccp4-6.0.99e/lib/clipper/clipper/mmdbold/clipper_mmdb_wrapper.cpp	2008-07-31 13:50:25.000000000 -0700
-@@ -40,7 +40,7 @@
- //L  MA 02111-1307 USA
- 
- #include "clipper_mmdb_wrapper.h"
--
-+#include <string.h>
- 
- namespace clipper {
- 
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-fix-setup-bash-incompatibility.patch b/sci-chemistry/ccp4-apps/files/6.1.3-fix-setup-bash-incompatibility.patch
deleted file mode 100644
index d98f54cdb3c1..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-fix-setup-bash-incompatibility.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4-6.0.99e.orig/include/ccp4.setup-bash	2008-07-31 10:37:22.000000000 -0700
-+++ ccp4-6.0.99e/include/ccp4.setup-bash	2008-07-31 12:47:14.000000000 -0700
-@@ -181,7 +181,7 @@
- 
- #Python path for the subprocess fixed module
- 
--if ($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-rename-rapper-ng.patch b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch
new file mode 100644
index 000000000000..a5144cfa5d33
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch
@@ -0,0 +1,60 @@
+diff --git a/src/Makefile.in b/src/Makefile.in
+index 70781f3..b2dcc25 100755
+--- a/src/Makefile.in
++++ b/src/Makefile.in
+@@ -760,7 +760,7 @@ chainsawobjs = chainsaw.o
+ pdbcur : $(pdbcurobjs)
+ 	@$(SETFLAGS) ; rm -f pdbcur; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o pdbcur $(pdbcurobjs) $(LDCXXFLAGS)
+ ncont : $(ncontobjs)
+-	@$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS)
++	@$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) -lmmdb
+ coord_format : $(coord_formatobjs)
+ 	@$(SETFLAGS) xxx=1 ; \
+ 	rm -f coord_format; \
+diff --git a/src/rapper/LOOP/Makefile.am b/src/rapper/LOOP/Makefile.am
+index 85f212e..2608c6d 100755
+--- a/src/rapper/LOOP/Makefile.am
++++ b/src/rapper/LOOP/Makefile.am
+@@ -15,12 +15,12 @@ params.cpp typed_value.cpp misc.cpp residue.cpp atom.cpp psa.cpp edm_sidechains.
+ 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
++rapper_LDADD = @GC_LIBS@ @LIBXML_LIBS@
+ 
+ pkgdatadir = $(datadir)/rapper
+ dist_pkgdata_DATA = params.xml
+ 
+-INCLUDES = -I. -I../gc7.0/include -I../libxml2/include
++INCLUDES = -I. @LIBXML_CFLAGS@ @GC_CFLAGS@
+ #SUBDIRS = \
+ #@PYTHON_USE_TRUE@ python
+ 
+diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am
+index e78b10d..486b931 100755
+--- a/src/rapper/Makefile.am
++++ b/src/rapper/Makefile.am
+@@ -1,3 +1,3 @@
+-SUBDIRS = libxml2 gc7.0 LOOP data
++SUBDIRS = LOOP data
+ 
+ EXTRA_DIST =
+diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac
+index 5e4ef69..268a579 100755
+--- a/src/rapper/configure.ac
++++ b/src/rapper/configure.ac
+@@ -48,6 +48,13 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno)
+ 
+ AC_SUBST(rapper_LDFLAGS)
+ 
+-AC_CONFIG_SUBDIRS([gc7.0 libxml2])
++PKG_CHECK_MODULES([LIBXML],[libxml-2.0])
++AC_SUBST([LIBXML_CFLAGS])
++AC_SUBST([LIBXML_LIBS])
++
++PKG_CHECK_MODULES([GC],[bdw-gc])
++AC_SUBST([GC_CFLAGS])
++AC_SUBST([GC_LIBS])
++
+ #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile)
+ AC_OUTPUT(Makefile LOOP/Makefile data/Makefile)
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
deleted file mode 100644
index a71c1354436c..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper.patch
+++ /dev/null
@@ -1,77 +0,0 @@
---- 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
deleted file mode 100644
index 43bfcf7c7a0e..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-rename-truncate.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-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
deleted file mode 100644
index c85c688debe4..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-setup.patch
+++ /dev/null
@@ -1,336 +0,0 @@
-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