ccp4 -- ccp4-apps

2 files changed, 16 insertions, 406 deletions

diff --git a/sci-chemistry/ccp4/Manifest b/sci-chemistry/ccp4/Manifest
index 5c7f98634..b21ae3e08 100644
--- a/sci-chemistry/ccp4/Manifest
+++ b/sci-chemistry/ccp4/Manifest
@@ -18,7 +18,6 @@ AUX 6.1.2-rename-truncate.patch 1515 RMD160 eff332faa67a1732e0f99cc6cdcb846932ea
 DIST 6.1.1-090511-updates.patch.bz2 8915 RMD160 58114b0ba6d225078044a8a6f9245aab66c6b572 SHA1 15c327c0b218b542b0c3955a9e63d2c6de299f7e SHA256 c0dbbde05b72f2460ada22f556d4cfe1f286a448ceb1181fd48b758468e509ac
 DIST ccp4-6.1.1-core-src.tar.gz 246661086 RMD160 6722367727e4b6b1f8456f1458c9aac124923a89 SHA1 9141801e021f8a5107ed1e3989840e4de849b39c SHA256 56f971e05fe4543173451e48600813492fd0081b25d4a659cb0fed1fd2529407
 DIST ccp4-6.1.1-src-patch-04_03_09.tar.gz 279642 RMD160 1a7c3b6cc846d315fc577e78b4aa00ab85a3d3d2 SHA1 29dbb84f3d63fc860694473ca99cf8bb71dae18a SHA256 eb806168235b55fbafdd72591ba94d35b78cc715a56a8b90979644d420ad672a
-DIST ccp4-6.1.2-core-src.tar.gz 247214086 RMD160 58acfc6f4bedfbea69379cf9155a3f199ff4b8d6 SHA1 47be9044be8b49f5ddee8e2f959d8439ae926a79 SHA256 ced18718198cc83370ba337b981bcb369c183850559240ba8256d93f487b13b0
 DIST ctruncate.cpp-r1.13.2.5-r1.13.2.7.diff 4993 RMD160 06deba4ffc19292d3c1b9136e380c8bf273d8311 SHA1 ce91a917547f03b699504b325aadfc4af1b3b51d SHA256 5eb6d6bfbc0197761864fa69062065639adfa8507c3ced99164afc0b5105132d
 EBUILD ccp4-6.1.1-r1.ebuild 11281 RMD160 523a351ef16aaa5a599ca081a9fa1a0f9d50319c SHA1 ab186ddc879f443fe8bf0db7b14001fe5e6dd3a0 SHA256 e92b2d21f1332f808b14f7cc9bcc04648d93983c5a50014e40b27b55b2578189
 EBUILD ccp4-6.1.1-r3.ebuild 11533 RMD160 75cf324436d1264af8cee88d7acdc3d61d1a1163 SHA1 034966380384691a05f60547b294b21167c04424 SHA256 2f195a63886488f0e1c7eedbd35c513805f9da224cb1272b82a61442e7027f9c
@@ -26,6 +25,6 @@ EBUILD ccp4-6.1.1-r4.ebuild 11487 RMD160 73c05354efb4e32495f8abda001354199939b5f
 EBUILD ccp4-6.1.1-r5.ebuild 11541 RMD160 baa8f0063fe798506c543fbed6c14557fa4a9b96 SHA1 19dfb2c04b8e335ddd073459724aadc0e55169b9 SHA256 f482d3f3680416b5d5287c024ecac89993c62f93b74a990784e0e03563f458d1
 EBUILD ccp4-6.1.1-r6.ebuild 11643 RMD160 41ec2ac76ddd724fedb4a850e0fad750f9856f17 SHA1 61a411ad26bcf50cd766318559e7b52f583a8515 SHA256 2e898b66a09e38aa26f2651ac25b053da075ee5be442c613ebf26c31d4d5c1ea
 EBUILD ccp4-6.1.1.ebuild 11078 RMD160 bdda0b25af939be1d59f1d25a3f5d1b603f8b17c SHA1 ceb05f4916197ca661660510e7eec70924032a1e SHA256 33214b5ca84c710112fb286de06073a843400fa2331715db1672713b33032024
-EBUILD ccp4-6.1.2.ebuild 11450 RMD160 952f35a05dfb2a5f6c0333a4f4bd0a6b148142da SHA1 574b9e6b66d71df2013c5d43d3bd0fa479891862 SHA256 bde7631e432f218c30e884c56daa011ede4877bee108ec880986d915014d9631
+EBUILD ccp4-6.1.2.ebuild 535 RMD160 6d151ead41bc0b309432688768031eab35d0b0ce SHA1 9faa74ed9dd01dbbfd8180af3ab52ca70c8ab144 SHA256 a506584eecf45ba2adc7c9ff8ea426f2993c5397f4401a88bab57d0a58278988
 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/ccp4-6.1.2.ebuild b/sci-chemistry/ccp4/ccp4-6.1.2.ebuild
index 6246f2ab2..bb0962522 100644
--- a/sci-chemistry/ccp4/ccp4-6.1.2.ebuild
+++ b/sci-chemistry/ccp4/ccp4-6.1.2.ebuild
@@ -2,412 +2,23 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-inherit fortran eutils gnuconfig toolchain-funcs autotools
-
-FORTRAN="g77 gfortran ifc"
-
-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"
+DESCRIPTION="Protein X-ray crystallography toolkit -- meta package"
 HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
-SRC_URI="${SRC}/${PV}/${P}-core-src.tar.gz"
-#	${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz
-#	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
+SRC_URI=""
 
 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.
-RDEPEND="X? (
-			x11-libs/libX11
-			x11-libs/libXt
-			x11-libs/libXaw
-			x11-libs/libxdl_view
-			x11-libs/libjwc_c
-			x11-libs/libjwc_f
-		)
-		>=dev-lang/tk-8.3
-		>=dev-tcltk/blt-2.4
-		virtual/lapack
-		virtual/blas
-		=sci-libs/fftw-2*
-		sci-chemistry/pdb-extract
-		sci-chemistry/rasmol
-		sci-libs/clipper
-		app-shells/tcsh
-		dev-python/pyxml
-		dev-libs/libxml2
-		dev-libs/boehm-gc
-		dev-tcltk/iwidgets
-		>=dev-tcltk/tdom-0.8
-		dev-tcltk/tkimg
-		dev-tcltk/tktreectrl
-		dev-tcltk/itcl
-		dev-tcltk/itk
-		sci-libs/ccp4-libs
-		!app-office/sc"
-DEPEND="${RDEPEND}
-		=sys-devel/automake-1.6*
-		X? (
-				x11-misc/imake
-				x11-proto/inputproto
-				x11-proto/xextproto
-		)"
-PDEPEND="sci-chemistry/mosflm
-	 sci-chemistry/imosflm
-	 sci-chemistry/molrep
-	 sci-chemistry/refmac
-	 sci-chemistry/xia2
-	 sci-chemistry/ccp4i
-	 sci-libs/balbes-db"
-
-S="${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
-
-#	epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	einfo "Applying Gentoo patches ..."
-	# These two only needed when attempting to install outside build dir via
-	# --bindir and --libdir instead of straight copying after build
-
-	# it attempts to install some libraries during the build
-	#ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch
-	# hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
-	# without this patch when --libdir is set
-	# Rotgen still needs more patching to find it
-	#ccp_patch "${FILESDIR}"/add-xdl-libdir.patch
-
-	# 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
-
-	# We already have sci-chemistry/pdb-extract
-# Use configure option instead
-#	ccp_patch "${FILESDIR}"/dont-build-pdb-extract.patch
-
-# Don't use these when we aren't building phaser
-#	ccp_patch "${FILESDIR}"/make-phaser-bindir.patch
-#	ccp_patch "${FILESDIR}"/no-phaser-ld-assume-kernel.patch
-#	# scons config.py tries to chmod python on live system
-#	ccp_patch "${FILESDIR}"/dont-chmod-python-binary.patch
-
-# Upstream fixed it
-	# csh syntax doesn't work in a bash script
-#	ccp_patch "${FILESDIR}"/${PV}-fix-setup-bash-incompatibility.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
-
-	# mosflm has its own ebuild
-#	ccp_patch "${FILESDIR}"/${PV}-dont-build-mosflm.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# glibc-2.10 getline fix
-	sed -e "s:getline:${PN}getline:g" -i lib/src/fsplit.c
-
-	# 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 "${S}"/include/ccp4.setup
-
-# Only needed when using --bindir and --libdir
-	# Needed to avoid errors. Originally tried to make lib and bin
-	# in configure script, now patched out by dont-make-dirs-in-configure.patch
-#	dodir /usr/include /usr/$(get_libdir) /usr/bin
-
-#	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"
-		"${S}"/include/ccp4.setup* || die
-
-	# Get rid of S instances
-	# Also the main clipper library is built as libclipper-core, not libclipper
-#	sed -i \
-#		-e "s:${S}:$usr:g" \
-#		-e "s:lclipper :lclipper-core :g" \
-#		"${S}"/bin/clipper-config || die
-#	sed -i \
-#		-e "s:${S}:usr:g" \
-#		"${S}"/$(get_libdir)/cctbx/cctbx_build/setpaths*
-
-	# Bins
-	dobin "${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
-
-	# balbes
-#	insinto /usr/share/ccp4
-#	doins -r "${S}"/share/balbes || die
-
-	# smartie -- log parsing
-	insinto /usr/share/ccp4
-	doins -r "${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}
-}
+IUSE=""
+
+RDEPEND="sci-chemistry/ccp4-apps
+	sci-chemistry/ccp4i
+	sci-chemistry/imosflm
+	sci-chemistry/molrep
+	sci-chemistry/mosflm
+	sci-chemistry/pdb-extract
+	sci-chemistry/rasmol
+	sci-chemistry/refmac
+	sci-chemistry/scala
+	sci-chemistry/xia2"
+DEPEND=""