ccp4 --> ccp4-apps

13 files changed, 906 insertions, 0 deletions

diff --git a/sci-chemistry/ccp4-apps/ChangeLog b/sci-chemistry/ccp4-apps/ChangeLog
new file mode 100644
index 000000000..5d239ff57
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/ChangeLog
@@ -0,0 +1,155 @@
+# ChangeLog for sci-chemistry/ccp4
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*ccp4-6.1.1-r6 (07 Jul 2009)
+
+  07 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +ccp4-6.1.1-r6.ebuild:
+  resort DEPENDENCIES
+
+*ccp4-6.1.1-r5 (05 Jul 2009)
+
+  05 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/6.1.1-noxia.patch, +ccp4-6.1.1-r5.ebuild:
+  noxia patch
+
+  02 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  ccp4-6.1.1-r4.ebuild:
+  userpriv usersandbox fix
+
+*ccp4-6.1.1-r4 (01 Jul 2009)
+
+  01 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  -ccp4-6.1.1-r2.ebuild, +ccp4-6.1.1-r4.ebuild:
+  first patch from upstram -- ctruncate
+  removed old version
+
+*ccp4-6.1.2 (01 Jul 2009)
+
+  01 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/6.1.2-clipper-mmdbold-ggc-4.3.patch,
+  +files/6.1.2-dont-build-double-and-make-bindir.patch,
+  +files/6.1.2-dont-build-libs.patch,
+  +files/6.1.2-dont-make-dirs-in-configure.patch,
+  +files/6.1.2-fix-setup-bash-incompatibility.patch,
+  +files/6.1.2-nomolref.patch, +files/6.1.2-rename-rapper.patch,
+  +ccp4-6.1.2.ebuild, +files/6.1.2-rename-truncate.patch:
+  new upstream release
+
+*ccp4-6.1.1-r3 (11 Jun 2009)
+
+  11 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/6.1.1-nomolref.patch, +ccp4-6.1.1-r3.ebuild:
+  We don't wat to install molref, because it is not provided as source and
+  linked against icc
+
+  11 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  ccp4-6.1.1-r2.ebuild:
+  examples are now optional vie USE="examples"
+
+*ccp4-6.1.1-r2 (03 Jun 2009)
+
+  03 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +ccp4-6.1.1-r2.ebuild:
+  glibc-2.10 getline fix
+
+*ccp4-6.1.1-r1 (13 May 2009)
+
+  13 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +ccp4-6.1.1-r1.ebuild:
+  Including updates from upstream 03/04/09
+  fixing bug 269504
+
+  27 Mar 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> ccp4-6.1.1.ebuild:
+  removed !media-libs/raptor as collision is fixed
+
+  12 Mar 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> ChangeLog:
+  rapper conflict with media-libs/raptor resolved
+
+  03 Jun 2008; Michael Sterrett <mr_bones_@gentoo.org> ccp4-6.0.1-r1.ebuild,
+  ccp4-6.0.2.ebuild, ccp4-6.0.2-r1.ebuild:
+  remove reference to app-shells/csh which has been removed
+
+  14 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>; ccp4-6.0.2-r1.ebuild:
+  Install examples (Justin Lecher).
+
+  13 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>; ccp4-6.0.2-r1.ebuild:
+  Try harder to remove rasmol man pages (Justin Lecher).
+
+  08 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>; ccp4-6.0.2-r1.ebuild:
+  Remove message about sourcing setup scripts.
+
+*ccp4-6.0.2-r1 (08 Apr 2008)
+
+  08 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/6.0.2-gcc-4.1.2-idate-fix.patch, +ccp4-6.0.2-r1.ebuild:
+  (#175630, #201150) Fix build. Install setup scripts into /etc/profile.d/
+  so they're sourced automatically upon login. In setup scripts, don't use
+  CLIBD before it's been set. Update to latest upstream patches. Deal with
+  non-gzip compression types.
+
+  22 Jul 2007; Donnie Berkholz <dberkholz@gentoo.org>; ccp4-6.0.1-r1.ebuild:
+  Drop virtual/x11 references.
+
+  02 Jul 2007; Piotr Jaroszyński <peper@gentoo.org> ccp4-6.0.1-r1.ebuild,
+  ccp4-6.0.2.ebuild:
+  (QA) RESTRICT clean up.
+
+  07 Apr 2007; Mike Frysinger <vapier@gentoo.org> ccp4-6.0.1-r1.ebuild,
+  ccp4-6.0.2.ebuild:
+  Convert *DESTTREE abuse into proper calls to the *into functions.
+
+  15 Mar 2007; Danny van Dyk <kugelfang@gentoo.org> ccp4-6.0.1-r1.ebuild,
+  ccp4-6.0.2.ebuild:
+  QA: Removed illegal use of ${ROOT}. Bug #168043
+
+  06 Jan 2007; Danny van Dyk <kugelfang@gentoo.org> -ccp4-6.0.1.ebuild:
+  QA: Removed unused versions.
+
+*ccp4-6.0.2 (24 Nov 2006)
+
+  24 Nov 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/6.0.2-dont-make-dirs-in-configure.patch,
+  +files/6.0.2-ppc-double-define-gerror.patch, +ccp4-6.0.2.ebuild:
+  Bump.
+
+  26 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; ccp4-6.0.1-r1.ebuild:
+  Stable on x86/ppc.
+
+  20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
+  (#148281) Change herd to sci-chemistry from sci.
+
+*ccp4-6.0.1-r1 (07 Aug 2006)
+
+  07 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  +ccp4-6.0.1-r1.ebuild:
+  Add upstream patches. The build system won't accept LDFLAGS, so unset them.
+  (#142183) Source the setup script again in src_install() to make sure CBIN
+  and CCP4_LIB get set. Not doing this breaks USE=X because the Imakefiles use
+  them. Stop changing the value of CCP4_LIB, that was only necessary for the
+  bindir=/usr/bin, libdir=/usr/libdir install, which was too much work.
+
+  05 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
+  Remove myself as maintainer, anyone feel free to work on this, although I'll
+  continue to do so as well.
+
+  07 Jul 2006; Donnie Berkholz <spyderous@gentoo.org>; metadata.xml:
+  Update to my new email address.
+
+*ccp4-6.0.1 (16 Jun 2006)
+
+  16 Jun 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/6.0.1-dont-make-dirs-in-configure.patch,
+  +files/6.0.1-ppc-double-define-gerror.patch,
+  +files/ccp4i-default-to-firefox.patch,
+  +files/check-blas-lapack-pthread.patch,
+  +files/clipper-find-mccp4-includes.patch,
+  +files/create-mosflm-bindir.patch, +files/dont-build-rasmol.patch,
+  +files/make-ipmosflm-dir.patch, +files/make-mosflm-cbf-libdir.patch,
+  +files/make-mosflm-index-libdir.patch, +files/make-mosflm-libdir.patch,
+  +files/pass-clipper-enablevals.patch, +metadata.xml, +ccp4-6.0.1.ebuild:
+  Add CCP4, a popular protein X-ray crystallography toolkit. Relies on portage
+  auto-fixing RPATHs for now, because its build system consists of a bunch of
+  stuff thrown together into the same tarball.
+
diff --git a/sci-chemistry/ccp4-apps/Manifest b/sci-chemistry/ccp4-apps/Manifest
new file mode 100644
index 000000000..53edbb4b1
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/Manifest
@@ -0,0 +1,13 @@
+AUX 6.1.2-clipper-mmdbold-ggc-4.3.patch 656 RMD160 6b302779b48217a14f5ac9110bc307db3a3b51eb SHA1 f5813d6769fa9dc11605425cdbda85691d3016bc SHA256 982eff0336a6dfaf4e280d51a59cf722fc063ca89d15ca0af46ce83727fb9a8a
+AUX 6.1.2-dont-build-double-and-make-bindir.patch 688 RMD160 f5f93cbec122ce81a1ddb1cf57a852d51fa5e5d6 SHA1 4c924554c5c1991ed691fe3474eeffbd108493a9 SHA256 037a3d9042c784c895083fe5348ed3bde74620c1b6b3b2cd4eea53bdbfe77d53
+AUX 6.1.2-dont-build-libs.patch 1255 RMD160 6454c2f61a13dbb8238b5ceed69c233fcf336ed4 SHA1 ff23480016731940279b8742707024f5a6e10bf3 SHA256 0d4a083d6c6bce38db0b84f9dccf0f339d746f9c0dd316eeb745f8427401be75
+AUX 6.1.2-dont-build-scala.patch 2195 RMD160 c09296e33acb2f10d69c8543163606d5867ba15f SHA1 a6bcbc519edeac0cfd47f677d8d6c79aa2a3b02a SHA256 73d4af040eef67e597b11877cc3719f5b15c5e357c3882449dc993a84857c4a3
+AUX 6.1.2-dont-make-dirs-in-configure.patch 2866 RMD160 ba49e45ab609a42a2d93b96f55af913bf9625610 SHA1 36c9329c3768c08687ef062c9ab649d32833b422 SHA256 1b5997f17526a4fd60ffa9eccf4b765aadf3a78c9394657000e0454f364240ca
+AUX 6.1.2-fix-setup-bash-incompatibility.patch 422 RMD160 e7e886ab030cf3324302c8fd0c866b48eeb34f8c SHA1 4e549abcd3ced1e6ecf9d3f2bddfed70425d61aa SHA256 109a0e806f9c0e1b8bf5e5f0c58be6f1dae06396b62ee4dae9f579ff7dcb5a01
+AUX 6.1.2-nomolref.patch 559 RMD160 93a81aec6548fa909c67546958878fc27632b392 SHA1 e16dafd552839128f81bc2e8e8f9953258e1c398 SHA256 1ba59db41f93c02494beb7a5d816dea966341009344805df4dfb873ab4e98eca
+AUX 6.1.2-rename-rapper.patch 2856 RMD160 37504bed3cb4e1858d88331305deef6564616b02 SHA1 31f513c987e1408b868f8c9de4aaa9f2c35cb378 SHA256 d9fed1ec65089c4130358aeed771b32c1253e48a73e90f0ce7b92bd0abbb0c2b
+AUX 6.1.2-rename-truncate.patch 1515 RMD160 eff332faa67a1732e0f99cc6cdcb846932eadc87 SHA1 b504542cf710e1b54a684b0fa0e8d73d967c96ac SHA256 50a59a1856867daa3de1f8f53e92bcfe74dea3a6d3c4ba238a9ea83dbcdfbf07
+DIST ccp4-6.1.2-core-src.tar.gz 247203373 RMD160 d2ead65da0a2561a8a256cdaa15a6b1a02b6d49e SHA1 fe94461fcafa7074231e01221760e24bb886d605 SHA256 875137beb74cb385b89fe3e49feeda78330c175861a590ee5f7cdbec26bc0e8a
+EBUILD ccp4-apps-6.1.2.ebuild 9836 RMD160 62d0a3645c7a9dab1ace1e8834c87a9e78e1bc2a SHA1 2c2ac770b68a41cae9c5178336bb7a19ed57cce6 SHA256 69985871961e839a12a0ca6fd4b0c0b746b310d436a87480c643b4da5cd1ad9a
+MISC ChangeLog 5725 RMD160 a561282ea9bd67da0b6e17eaaf47d559c711b055 SHA1 23ba90946cda15225ebabf48309e41267d30f22e SHA256 0b9ab8e5fe091a7a79a394c355e7d253711b08f7f0ce4fbb65e4860d30229308
+MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.2.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.2.ebuild
new file mode 100644
index 000000000..7426bfff7
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.2.ebuild
@@ -0,0 +1,374 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit fortran eutils 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"
+# plain files which were copied over
+	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
+# real patches
+	[[ -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="X examples"
+
+# app-office/sc overlaps sc binary and man page
+# We can't rename ours since the automated ccp4i interface expects it there,
+# as do many scripts. app-office/sc can't rename its because that's the name
+# of the package.
+X11DEPS="x11-libs/libX11
+	x11-libs/libXt
+	x11-libs/libXaw
+	x11-libs/libxdl_view
+	x11-libs/libjwc_c
+	x11-libs/libjwc_f"
+
+TKDEPS=">=dev-lang/tk-8.3
+	>=dev-tcltk/blt-2.4
+	dev-tcltk/iwidgets
+	>=dev-tcltk/tdom-0.8
+	dev-tcltk/tkimg
+	dev-tcltk/tktreectrl
+	dev-tcltk/itcl
+	dev-tcltk/itk"
+
+SCILIBS="sci-libs/ccp4-libs
+	virtual/lapack
+	virtual/blas
+	=sci-libs/fftw-2*
+	sci-libs/clipper
+	sci-libs/balbes-db"
+
+SCIAPPS="sci-chemistry/pdb-extract
+	sci-chemistry/rasmol"
+
+
+DEPEND="X? ( ${X11DEPS} )
+	${TKDEPS}
+	${SCILIBS}
+	${SCIAPPS}
+	app-shells/tcsh
+	dev-python/pyxml
+	dev-libs/libxml2
+	dev-libs/boehm-gc
+	!app-office/sc"
+DEPEND="${RDEPEND}
+	=sys-devel/automake-1.6*
+	X? (
+		x11-misc/imake
+		x11-proto/inputproto
+		x11-proto/xextproto
+	)"
+
+S="${WORKDIR}/${PN}-${PV}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	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}-nomolref.patch
+
+	# We build scala ourself
+	ccp_patch "${FILESDIR}"/${PV}-dont-build-scala.patch
+
+	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::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_compile() {
+	# Build system is broken if we set LDFLAGS
+	unset LDFLAGS
+
+	# 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~^\(setenv CCP4I_TCLTK.*\)/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}
+
+	# Can't use econf, configure rejects unknown options like --prefix
+	./configure \
+		$(use_enable X x) \
+		--with-shared-libs \
+		--with-fftw=/usr \
+		--with-warnings \
+		--disable-pdb_extract \
+		--disable-cctbx \
+		--disable-phaser \
+		--disable-clipper \
+		--disable-mrbump \
+		--tmpdir="${TMPDIR}" \
+		${GENTOO_OSNAME} || die "econf failed"
+
+	# fsplit is required for the programs
+	pushd lib/src 2>/dev/null
+	emake fsplit -j1 || die
+	popd 2>/dev/null
+
+	# We do this manually, since disabling the clipper libraries also
+	# disables the clipper programs
+	pushd src/clipper_progs 2>/dev/null
+	econf \
+		--prefix="${S}" \
+		--with-ccp4="${S}" \
+		--with-clipper=/usr \
+		--with-fftw=/usr \
+		--with-mmdb=/usr \
+		CXX=$(tc-getCXX) \
+		|| die
+	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
+	sed -i \
+		-e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \
+		-e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
+		-e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
+		-e "s~^\(setenv DBCCP4I_TOP\).*~\1 \$CCP4/share/ccp4/dbccp4i~g" \
+		-e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
+		-e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \
+		-e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
+		-e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
+		-e "s~^\(.*setenv PYTHONPATH .*\)\$CCP4.*~\1\$CCP4/share/ccp4/python~g" \
+		-e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \
+		"${S}"/include/ccp4.setup* || die
+
+	# Don't check for updates on every sourcing of /etc/profile
+	sed -i \
+		-e "s:\(eval python.*\):#\1:g"
+		"${S}"/include/ccp4.setup* || die
+
+	# Bins
+	dobin "${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 ${file} || die
+		fi
+	done
+
+	# Setup scripts
+	insinto /etc/profile.d
+	newins "${S}"/include/ccp4.setup-bash ccp4.setup.sh || die
+	newins "${S}"/include/ccp4.setup-dist ccp4.setup.csh || die
+	rm -f "${S}"/include/ccp4.setup-bash
+	rm -f "${S}"/include/ccp4.setup-dist
+
+	# Environment files, setup scripts, etc.
+	insinto /usr/share/ccp4/include
+	doins "${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 "${S}"/manual/*
+
+	dodoc "${S}"/README "${S}"/CHANGES
+
+	dodoc "${S}"/doc/*
+	rm "${D}"/usr/share/doc/${PF}/GNUmakefile.*
+	rm "${D}"/usr/share/doc/${PF}/COPYING.*
+
+	dohtml -r "${S}"/html/*
+	dodoc "${S}"/examples/README
+
+	# Fix wrongly installed HTML pages from clipper
+	dohtml "${D}"/usr/html/*
+	rm -rf "${D}"/usr/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
+}
+
+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/6.1.2-clipper-mmdbold-ggc-4.3.patch b/sci-chemistry/ccp4-apps/files/6.1.2-clipper-mmdbold-ggc-4.3.patch
new file mode 100644
index 000000000..66186609a
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/files/6.1.2-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/6.1.2-dont-build-double-and-make-bindir.patch b/sci-chemistry/ccp4-apps/files/6.1.2-dont-build-double-and-make-bindir.patch
new file mode 100644
index 000000000..e62ae12ad
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/files/6.1.2-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/6.1.2-dont-build-libs.patch b/sci-chemistry/ccp4-apps/files/6.1.2-dont-build-libs.patch
new file mode 100644
index 000000000..5859093e7
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/files/6.1.2-dont-build-libs.patch
@@ -0,0 +1,35 @@
+--- ./Makefile.in.orig	2008-08-01 10:27:23.000000000 -0700
++++ ./Makefile.in	2008-08-01 14:30:22.000000000 -0700
+@@ -3,7 +3,7 @@
+ # $Header: /nfs/ccpdisk/xtal/CVSROOT/ccp4/Makefile.in,v 1.57 2008/04/09 10:41:58 fr45 Exp $
+ 
+ SHELL = /bin/sh
+-DIRS = $(fftwdir) $(clipperdir) $(diffimdir) $(lapackdir) $(ccifdir) lib/src $(ssmdir) src lib/data unsupported/src x-windows share $(prereleasedir)
++DIRS = src lib/data unsupported/src x-windows share $(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
+@@ -67,19 +67,19 @@
+ 	$(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/6.1.2-dont-build-scala.patch b/sci-chemistry/ccp4-apps/files/6.1.2-dont-build-scala.patch
new file mode 100644
index 000000000..9e7b794bd
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/files/6.1.2-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 chef \
++         dm dmmulti stereo mapmask maprot ncsmask chef \
+          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/6.1.2-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.2-dont-make-dirs-in-configure.patch
new file mode 100644
index 000000000..583697cea
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/files/6.1.2-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 $i/Makefile.in
++#       fi
++#     fi
++#   done
++#fi
+ 
+ ### sanity checks
+ 
diff --git a/sci-chemistry/ccp4-apps/files/6.1.2-fix-setup-bash-incompatibility.patch b/sci-chemistry/ccp4-apps/files/6.1.2-fix-setup-bash-incompatibility.patch
new file mode 100644
index 000000000..d98f54cdb
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/files/6.1.2-fix-setup-bash-incompatibility.patch
@@ -0,0 +1,11 @@
+--- ccp4-6.0.99e.orig/include/ccp4.setup-bash	2008-07-31 10:37:22.000000000 -0700
++++ ccp4-6.0.99e/include/ccp4.setup-bash	2008-07-31 12:47:14.000000000 -0700
+@@ -181,7 +181,7 @@
+ 
+ #Python path for the subprocess fixed module
+ 
+-if ($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/6.1.2-nomolref.patch b/sci-chemistry/ccp4-apps/files/6.1.2-nomolref.patch
new file mode 100644
index 000000000..f16b0ecb9
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/files/6.1.2-nomolref.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 = $(datadir)/pisa
+ 
+--- src/pisa/Makefile.in	2009-06-12 21:12:08.000000000 +0200
++++ src/pisa/Makefile.in.new	2009-06-12 21:41:52.000000000 +0200
+@@ -82,7 +82,7 @@
+ am__quote = @am__quote@
+ install_sh = @install_sh@
+ pisa_LDFLAGS = @pisa_LDFLAGS@
+-SUBDIRS = molref pisastore sbase
++SUBDIRS = pisastore sbase
+ 
+ dist_pkgdata_DATA = pisa.cfg
+ 
diff --git a/sci-chemistry/ccp4-apps/files/6.1.2-rename-rapper.patch b/sci-chemistry/ccp4-apps/files/6.1.2-rename-rapper.patch
new file mode 100644
index 000000000..a71c13544
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/files/6.1.2-rename-rapper.patch
@@ -0,0 +1,77 @@
+--- src/rapper/LOOP/Makefile.in	2008-05-29 16:39:40.000000000 +0200
++++ src/rapper/LOOP/Makefile.in.new	2009-03-12 20:40:03.157602172 +0100
+@@ -111,9 +111,9 @@
+ pyexecdir = @pyexecdir@
+ pythondir = @pythondir@
+ rapper_LDFLAGS = @rapper_LDFLAGS@
+-bin_PROGRAMS = rapper
++bin_PROGRAMS = rappermc
+ 
+-rapper_SOURCES = \
++rappermc_SOURCES = \
+ kip.h aaconv.cpp atomconv.cpp kip_snake.cpp \
+ kip_pdb.cpp measure.cpp lib_frags.cpp ran2.cpp \
+ heap.cpp queue.cpp 3Dgeom.cpp space_grid.cpp list.cpp search_residue.cpp bitfield.cpp \
+@@ -129,7 +129,7 @@
+ residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp
+ 
+ 
+-rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la
++rappermc_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la
+ dist_pkgdata_DATA = params.xml
+ 
+ INCLUDES = -I. -I../gc7.0/include -I../libxml2/include
+@@ -139,7 +139,7 @@
+ bin_PROGRAMS = rapper$(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/6.1.2-rename-truncate.patch b/sci-chemistry/ccp4-apps/files/6.1.2-rename-truncate.patch
new file mode 100644
index 000000000..43bfcf7c7
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/files/6.1.2-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/metadata.xml b/sci-chemistry/ccp4-apps/metadata.xml
new file mode 100644
index 000000000..9ac9ffdb3
--- /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>