sci-chemistry/ccp4 patch cleanup

sci-chemiszty/chooch added
sci-libs/cgraph added

27 files changed, 588 insertions, 110 deletions

diff --git a/sci-chemistry/ccp4/Manifest b/sci-chemistry/ccp4/Manifest
index 06a167095..2ede57037 100644
--- a/sci-chemistry/ccp4/Manifest
+++ b/sci-chemistry/ccp4/Manifest
@@ -1,25 +1,25 @@
-AUX 6.0.1-dont-make-dirs-in-configure.patch 2790 RMD160 904e37ab1ea20dda50f50ce8780268eb5fa52480 SHA1 f8989cb867c92def86ccd88b4d67f38578d5d80b SHA256 2dbf78513ef94d88e446042e969644ad8a8462a22e80105e7481af93003a18bf
-AUX 6.0.1-ppc-double-define-gerror.patch 424 RMD160 4f012233446fffa61e8d775a19a0dacea4ae2234 SHA1 209fa1bdf1e59b4055177e343b69e487d9183fb3 SHA256 09c2c1e0176bee94673b21609b2b00118b2bb4f5942f3feb35c64c61c99ebc61
-AUX 6.0.2-dont-make-dirs-in-configure.patch 2790 RMD160 904e37ab1ea20dda50f50ce8780268eb5fa52480 SHA1 f8989cb867c92def86ccd88b4d67f38578d5d80b SHA256 2dbf78513ef94d88e446042e969644ad8a8462a22e80105e7481af93003a18bf
-AUX 6.0.2-gcc-4.1.2-idate-fix.patch 433 RMD160 3ff2a25ed4698bfc33a074bef8d181ea98011061 SHA1 5ec002a974e04ba401b1207c9322fe6218998971 SHA256 331f0666f3163596ce2fce3385a216458f5455f50cd5130c84a24f3b741704c1
-AUX 6.0.2-ppc-double-define-gerror.patch 424 RMD160 4f012233446fffa61e8d775a19a0dacea4ae2234 SHA1 209fa1bdf1e59b4055177e343b69e487d9183fb3 SHA256 09c2c1e0176bee94673b21609b2b00118b2bb4f5942f3feb35c64c61c99ebc61
 AUX 6.1.1-clipper-mmdbold-ggc-4.3.patch 656 RMD160 6b302779b48217a14f5ac9110bc307db3a3b51eb SHA1 f5813d6769fa9dc11605425cdbda85691d3016bc SHA256 982eff0336a6dfaf4e280d51a59cf722fc063ca89d15ca0af46ce83727fb9a8a
+AUX 6.1.1-dont-build-double-and-make-bindir.patch 688 RMD160 f5f93cbec122ce81a1ddb1cf57a852d51fa5e5d6 SHA1 4c924554c5c1991ed691fe3474eeffbd108493a9 SHA256 037a3d9042c784c895083fe5348ed3bde74620c1b6b3b2cd4eea53bdbfe77d53
 AUX 6.1.1-dont-build-libs.patch 1255 RMD160 6454c2f61a13dbb8238b5ceed69c233fcf336ed4 SHA1 ff23480016731940279b8742707024f5a6e10bf3 SHA256 0d4a083d6c6bce38db0b84f9dccf0f339d746f9c0dd316eeb745f8427401be75
-AUX 6.1.1-dont-build-mosflm.patch 524 RMD160 b560ceb44ecb334f2de60db33cc20a5d9e1f8108 SHA1 652c34e1b3c465d45fd563d130396a08afe04bad SHA256 b39a188cb5722d3fb2709ebc6eb7a32ee199b5d4c71a7a12b22abe90b65434f7
-AUX 6.1.1-dont-build-rasmol-and-make-bindir.patch 680 RMD160 00fc4c92a8edbf31a5e0d0eeda702c4f6f536b40 SHA1 d2710f215d7b8eaec54eba880f39a1ecb84a583c SHA256 a33fd345b19238259c1f4186600c41764678a9e8bcd0adde6029b1c428af2438
 AUX 6.1.1-dont-make-dirs-in-configure.patch 2866 RMD160 ba49e45ab609a42a2d93b96f55af913bf9625610 SHA1 36c9329c3768c08687ef062c9ab649d32833b422 SHA256 1b5997f17526a4fd60ffa9eccf4b765aadf3a78c9394657000e0454f364240ca
 AUX 6.1.1-fix-setup-bash-incompatibility.patch 422 RMD160 e7e886ab030cf3324302c8fd0c866b48eeb34f8c SHA1 4e549abcd3ced1e6ecf9d3f2bddfed70425d61aa SHA256 109a0e806f9c0e1b8bf5e5f0c58be6f1dae06396b62ee4dae9f579ff7dcb5a01
-AUX ccp4i-default-to-firefox.patch 717 RMD160 626050c2ca8386e369900225f74f97fb22c3a91e SHA1 dc255e30033d1dbc422dbacd2c1814c13a003bc3 SHA256 40bc277d9353f13b490291fe0ba10c1180adc80a660afa5cf8f7c9449af909ae
-AUX check-blas-lapack-pthread.patch 5335 RMD160 d9818cd59333c6f40984f71a0f32249725d5ffcc SHA1 5aa0ee530975bd89dde38145297c4868ee54adbb SHA256 82a73295274b6d4cabbe00883a3e9cf6a38fe80eed8c487cd67960d073cb1231
-AUX clipper-find-mccp4-includes.patch 491 RMD160 203cb5f807ede5462070d993f3e4b914992aa3e1 SHA1 f58ef6f143d751d50b55e620be877327af651fb9 SHA256 154c012c0ca75fc0da50b412b948acec53f4cecd2efd8910af73166db270e026
-AUX create-mosflm-bindir.patch 438 RMD160 b0a210bf86de3af52c538efdf05d9ba44d7824d9 SHA1 30f45f7ac2eda5241256d31ee5073594985e5a05 SHA256 41b06cb4860b263fbc5c7c5be2aec1f859ff1cd6dd3750e5aae0410c264b1d84
-AUX dont-build-rasmol.patch 725 RMD160 2c294c46dcea586026e6d7c3936527e490bd7569 SHA1 97ac86575512776ecabb32488df6f59cf2431884 SHA256 f46b1d8d6f239f4b7c9b1d343661c98f1bc0015bc988881261b06a79a1e0c3e5
-AUX make-ipmosflm-dir.patch 375 RMD160 b359ff3028777157f6ce4cb60c5aa35b8177779e SHA1 1c23f2d56a8cfea479f5b32c842fe50d134c68c0 SHA256 2ca03ea4b4c1581be56bbac0afd3cbfe789b61a8453e50b1b477b074c6b2fd43
-AUX make-mosflm-cbf-libdir.patch 415 RMD160 19e275563cbd7c3d6b91630f8c554494a75d8ea0 SHA1 d264cbee4db1a1f48297ce43fef4f45e14e1aebe SHA256 475eec831306d33871f65b827b07a09dbe0ecd7b4f9e6af34a91fa4d433d56a4
-AUX make-mosflm-index-libdir.patch 358 RMD160 772bad5d83385adce5858f43ac9302c94cd6a6b8 SHA1 b889d238b0f3e2385ad8259ea4ea85b29d05e0d1 SHA256 5549d5208548168c0f246606802c143bd34b87ca3eb25640c6b777d9d9e4b902
-AUX make-mosflm-libdir.patch 371 RMD160 2ff9ddcc064b2621d241850d9774961b140d28b8 SHA1 0a4aba167b530544f6e602dab622e51fae1c7b68 SHA256 55c2978125acb3f1ba55039d171b09b6dbd13ee1dd1e4c1e48edc48e89d5c717
-AUX pass-clipper-enablevals.patch 501 RMD160 23466922268a91570b0f64cf79809b988e32689b SHA1 c254d31fe88ed1716a53bd549cf7aee537ca5204 SHA256 d476c9f231fb6cdfb5e57004b393644a88016318cdeed9c33c32de25e0d91b79
+AUX delete/6.0.1-dont-make-dirs-in-configure.patch 2790 RMD160 904e37ab1ea20dda50f50ce8780268eb5fa52480 SHA1 f8989cb867c92def86ccd88b4d67f38578d5d80b SHA256 2dbf78513ef94d88e446042e969644ad8a8462a22e80105e7481af93003a18bf
+AUX delete/6.0.1-ppc-double-define-gerror.patch 424 RMD160 4f012233446fffa61e8d775a19a0dacea4ae2234 SHA1 209fa1bdf1e59b4055177e343b69e487d9183fb3 SHA256 09c2c1e0176bee94673b21609b2b00118b2bb4f5942f3feb35c64c61c99ebc61
+AUX delete/6.0.2-dont-make-dirs-in-configure.patch 2790 RMD160 904e37ab1ea20dda50f50ce8780268eb5fa52480 SHA1 f8989cb867c92def86ccd88b4d67f38578d5d80b SHA256 2dbf78513ef94d88e446042e969644ad8a8462a22e80105e7481af93003a18bf
+AUX delete/6.0.2-gcc-4.1.2-idate-fix.patch 433 RMD160 3ff2a25ed4698bfc33a074bef8d181ea98011061 SHA1 5ec002a974e04ba401b1207c9322fe6218998971 SHA256 331f0666f3163596ce2fce3385a216458f5455f50cd5130c84a24f3b741704c1
+AUX delete/6.0.2-ppc-double-define-gerror.patch 424 RMD160 4f012233446fffa61e8d775a19a0dacea4ae2234 SHA1 209fa1bdf1e59b4055177e343b69e487d9183fb3 SHA256 09c2c1e0176bee94673b21609b2b00118b2bb4f5942f3feb35c64c61c99ebc61
+AUX delete/ccp4i-default-to-firefox.patch 717 RMD160 626050c2ca8386e369900225f74f97fb22c3a91e SHA1 dc255e30033d1dbc422dbacd2c1814c13a003bc3 SHA256 40bc277d9353f13b490291fe0ba10c1180adc80a660afa5cf8f7c9449af909ae
+AUX delete/check-blas-lapack-pthread.patch 5335 RMD160 d9818cd59333c6f40984f71a0f32249725d5ffcc SHA1 5aa0ee530975bd89dde38145297c4868ee54adbb SHA256 82a73295274b6d4cabbe00883a3e9cf6a38fe80eed8c487cd67960d073cb1231
+AUX delete/clipper-find-mccp4-includes.patch 491 RMD160 203cb5f807ede5462070d993f3e4b914992aa3e1 SHA1 f58ef6f143d751d50b55e620be877327af651fb9 SHA256 154c012c0ca75fc0da50b412b948acec53f4cecd2efd8910af73166db270e026
+AUX delete/create-mosflm-bindir.patch 438 RMD160 b0a210bf86de3af52c538efdf05d9ba44d7824d9 SHA1 30f45f7ac2eda5241256d31ee5073594985e5a05 SHA256 41b06cb4860b263fbc5c7c5be2aec1f859ff1cd6dd3750e5aae0410c264b1d84
+AUX delete/dont-build-rasmol.patch 725 RMD160 2c294c46dcea586026e6d7c3936527e490bd7569 SHA1 97ac86575512776ecabb32488df6f59cf2431884 SHA256 f46b1d8d6f239f4b7c9b1d343661c98f1bc0015bc988881261b06a79a1e0c3e5
+AUX delete/make-ipmosflm-dir.patch 375 RMD160 b359ff3028777157f6ce4cb60c5aa35b8177779e SHA1 1c23f2d56a8cfea479f5b32c842fe50d134c68c0 SHA256 2ca03ea4b4c1581be56bbac0afd3cbfe789b61a8453e50b1b477b074c6b2fd43
+AUX delete/make-mosflm-cbf-libdir.patch 415 RMD160 19e275563cbd7c3d6b91630f8c554494a75d8ea0 SHA1 d264cbee4db1a1f48297ce43fef4f45e14e1aebe SHA256 475eec831306d33871f65b827b07a09dbe0ecd7b4f9e6af34a91fa4d433d56a4
+AUX delete/make-mosflm-index-libdir.patch 358 RMD160 772bad5d83385adce5858f43ac9302c94cd6a6b8 SHA1 b889d238b0f3e2385ad8259ea4ea85b29d05e0d1 SHA256 5549d5208548168c0f246606802c143bd34b87ca3eb25640c6b777d9d9e4b902
+AUX delete/make-mosflm-libdir.patch 371 RMD160 2ff9ddcc064b2621d241850d9774961b140d28b8 SHA1 0a4aba167b530544f6e602dab622e51fae1c7b68 SHA256 55c2978125acb3f1ba55039d171b09b6dbd13ee1dd1e4c1e48edc48e89d5c717
+AUX delete/pass-clipper-enablevals.patch 501 RMD160 23466922268a91570b0f64cf79809b988e32689b SHA1 c254d31fe88ed1716a53bd549cf7aee537ca5204 SHA256 d476c9f231fb6cdfb5e57004b393644a88016318cdeed9c33c32de25e0d91b79
 DIST ccp4-6.1.1-core-src.tar.gz 246661086 RMD160 6722367727e4b6b1f8456f1458c9aac124923a89 SHA1 9141801e021f8a5107ed1e3989840e4de849b39c SHA256 56f971e05fe4543173451e48600813492fd0081b25d4a659cb0fed1fd2529407
-EBUILD ccp4-6.1.1.ebuild 11139 RMD160 9f296ec26cb851b7d1ae2cfcc375ba0a940f74ee SHA1 6d306f8d4d272702a76c5c9ed551604101da1f2a SHA256 db5868538910fe57a3e29cb1566fd36c912a654997e516e5d0cc227230c03406
+EBUILD ccp4-6.1.1.ebuild 11337 RMD160 12bc4dd2c12bd3b7f00565601f0a28a18f8896d2 SHA1 a69022fc4274acf0a051e7b90640755e65dd671a SHA256 57a920fa2a7ccb9fc6e6bbd342cf82f2422a408b77bcf4e1d46b7f497fc9b139
 MISC ChangeLog 3822 RMD160 f2895ef49e026b7b9dbb10bf54c2d2befe790ac0 SHA1 05df732a9f2d7b2b8f383d8543bb8020f0fa4239 SHA256 079c2aa96ec9dea37539bb1f79826ea8b6d22f1a4762cf669b9558eff3d43da5
+MISC ccp4-6.1.1.ebuild.bak 11236 RMD160 8302fbd908c232db05007d73df99a5e9cdf8db23 SHA1 886cf6325860ddacffb3cf28c1dda59260bbbb55 SHA256 5f83697c23bcb7195c3c6f52d8bc50d479718aea13aca77efc6643170846ade4
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-chemistry/ccp4/ccp4-6.1.1.ebuild b/sci-chemistry/ccp4/ccp4-6.1.1.ebuild
index d0aeabad6..a4782610d 100644
--- a/sci-chemistry/ccp4/ccp4-6.1.1.ebuild
+++ b/sci-chemistry/ccp4/ccp4-6.1.1.ebuild
@@ -44,6 +44,9 @@ 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
@@ -74,6 +77,7 @@ DEPEND="${RDEPEND}
 		)"
 PDEPEND="sci-chemistry/mosflm
 	 sci-chemistry/imosflm
+	 sci-chemistry/molrep
 	 sci-chemistry/refmac
 	 sci-chemistry/xia2
 	 sci-chemistry/ccp4i
@@ -83,15 +87,15 @@ S="${WORKDIR}/${PN}-${PV}"
 
 src_unpack() {
 	unpack ${A}
-	cd ${S}
+	cd "${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}
+		pushd "${dir}" >& /dev/null
+		ccp_patch ${DISTDIR}/"${p}"
 		popd >& /dev/null
 	done
 	einfo "Done."
@@ -102,44 +106,44 @@ src_unpack() {
 	# --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
+	#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 ${FILESDIR}/add-xdl-libdir.patch
+	#ccp_patch "${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
+	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-rasmol-and-make-bindir.patch
+	ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch
 
 	# We already have sci-chemistry/pdb-extract
 # Use configure option instead
-#	ccp_patch ${FILESDIR}/dont-build-pdb-extract.patch
+#	ccp_patch "${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 ${FILESDIR}/no-phaser-ld-assume-kernel.patch
+#	ccp_patch "${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 ${FILESDIR}/dont-chmod-python-binary.patch
+#	ccp_patch "${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
+#	ccp_patch "${FILESDIR}"/${PV}-fix-setup-bash-incompatibility.patch
 
 	# libraries come from sci-libs/ccp4-libs
-	ccp_patch ${FILESDIR}/${PV}-dont-build-libs.patch
+	ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch
 
 	# mosflm has its own ebuild
-	ccp_patch ${FILESDIR}/${PV}-dont-build-mosflm.patch
+#	ccp_patch "${FILESDIR}"/${PV}-dont-build-mosflm.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::g" configure
+	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
@@ -184,21 +188,21 @@ src_compile() {
 	# Sets up env
 	ln -s \
 		ccp4.setup-bash \
-		${S}/include/ccp4.setup
+		"${S}"/include/ccp4.setup
 
 	# We agree to the license by emerging this, set in LICENSE
 	sed -i \
 		-e "s~^\(^agreed=\).*~\1yes~g" \
-		${S}/configure
+		"${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" \
-		${S}/include/ccp4.setup*
+		"${S}"/include/ccp4.setup*
 
 	# Set up variables for build
-	source ${S}/include/ccp4.setup
+	source "${S}"/include/ccp4.setup
 
 	export CC=$(tc-getCC)
 	export CXX=$(tc-getCXX)
@@ -232,7 +236,7 @@ src_compile() {
 
 src_install() {
 	# Set up variables for build
-	source ${S}/include/ccp4.setup
+	source "${S}"/include/ccp4.setup
 
 # Only needed when using --bindir and --libdir
 	# Needed to avoid errors. Originally tried to make lib and bin
@@ -257,28 +261,28 @@ src_install() {
 		-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~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \
-		${S}/include/ccp4.setup* || die
+		"${S}"/include/ccp4.setup* || die
 
 	# Don't check for updates on every sourcing of /etc/profile
 	sed -i \
 		-e "s:\(eval python.*\):#\1:g"
-		${S}/include/ccp4.setup*
+		"${S}"/include/ccp4.setup*
 
 	# 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}:$usr:g" \
+#		-e "s:lclipper :lclipper-core :g" \
+#		"${S}"/bin/clipper-config || die
 #	sed -i \
 #		-e "s:${S}:usr:g" \
-#		${S}/$(get_libdir)/cctbx/cctbx_build/setpaths*
+#		"${S}"/$(get_libdir)/cctbx/cctbx_build/setpaths*
 
 	# Bins
-	dobin ${S}/bin/* || die
+	dobin "${S}"/bin/* || die
 
 	# Libs
-	for file in ${S}/lib/*; do
+	for file in "${S}"/lib/*; do
 		if [[ -d ${file} ]]; then
 			continue
 		elif [[ -x ${file} ]]; then
@@ -292,7 +296,7 @@ src_install() {
 	# Fix libdir in all *.la files
 	sed -i \
 		-e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
-		${D}/usr/$(get_libdir)/*.la
+		"${D}"/usr/$(get_libdir)/*.la
 
 	# Library symlinks
 	local LIBNAMES="libjwc_c.so.0.1.1
@@ -306,38 +310,38 @@ src_install() {
 
 	# 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 ${S}/include/ccp4.setup-dist
+	newins "${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 ${S}/include/* || die
+	doins "${S}"/include/* || die
 
 	# balbes
 #	insinto /usr/share/ccp4
-#	doins -r ${S}/share/balbes || die
+#	doins -r "${S}"/share/balbes || die
 
 	# smartie -- log parsing
 	insinto /usr/share/ccp4
-	doins -r ${S}/share/smartie || die
+	doins -r "${S}"/share/smartie || die
 
 	# Install docs and examples
 
-	doman ${S}/man/cat1/*
+	doman "${S}"/man/cat1/*
 
-	mv ${S}/manual/README ${S}/manual/README-manual
-	dodoc ${S}/manual/*
+	mv "${S}"/manual/README "${S}"/manual/README-manual
+	dodoc "${S}"/manual/*
 
-	dodoc ${S}/README ${S}/CHANGES
+	dodoc "${S}"/README "${S}"/CHANGES
 
-	dodoc ${S}/doc/*
-	rm ${D}/usr/share/doc/${PF}/GNUmakefile.*
-	rm ${D}/usr/share/doc/${PF}/COPYING.*
+	dodoc "${S}"/doc/*
+	rm "${D}"/usr/share/doc/${PF}/GNUmakefile.*
+	rm "${D}"/usr/share/doc/${PF}/COPYING.*
 
-	dohtml -r ${S}/html/*
-	dodoc ${S}/examples/README
+	dohtml -r "${S}"/html/*
+	dodoc "${S}"/examples/README
 
 	# Fix wrongly installed HTML pages from clipper
 	dohtml "${D}"/usr/html/*
@@ -345,19 +349,19 @@ src_install() {
 
 	for i in data rnase toxd; do
 		docinto examples/${i}
-		dodoc ${S}/examples/${i}/*
+		dodoc "${S}"/examples/${i}/*
 	done
 
 	docinto examples/tutorial
-	dohtml -r ${S}/examples/tutorial/html examples/tutorial/tut.css
+	dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css
 	for i in data results; do
 		docinto examples/tutorial/${i}
-		dodoc ${S}/examples/tutorial/${i}/*
+		dodoc "${S}"/examples/tutorial/${i}/*
 	done
 
 	for i in non-runnable runnable; do
 		docinto examples/unix/${i}
-		dodoc ${S}/examples/unix/${i}/*
+		dodoc "${S}"/examples/unix/${i}/*
 	done
 
 	# Needed for ccp4i docs to work
@@ -365,7 +369,7 @@ src_install() {
 	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html
 
 	# Fix overlaps with other packages
-	rm -f ${D}/usr/share/man/man1/rasmol.1.* ${D}/usr/lib/font84.dat || die
+	rm -f "${D}"/usr/share/man/man1/rasmol.1* "${D}"/usr/lib/font84.dat || die
 }
 
 pkg_postinst() {
@@ -373,6 +377,7 @@ pkg_postinst() {
 	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/ccp4-6.1.1.ebuild.bak b/sci-chemistry/ccp4/ccp4-6.1.1.ebuild.bak
new file mode 100644
index 000000000..24f07eae5
--- /dev/null
+++ b/sci-chemistry/ccp4/ccp4-6.1.1.ebuild.bak
@@ -0,0 +1,415 @@
+# 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"
+
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
+
+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}/source/${P}-core-src.tar.gz"
+SRC_URI="${SRC}/6.1.1/${P}-core-src.tar.gz"
+#	${SRC}/6.1/${P}-phaser-src.tar.gz
+#	${SRC}/6.1/${P}-balbes_db.tar.gz"
+for i in $(seq $PATCH_TOT); do
+	NAME="PATCH${i}[1]"
+	SRC_URI="${SRC_URI}
+		${SRC}/${PV}/patches/${!NAME}"
+done
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="X"
+# app-office/sc overlaps sc binary and man page
+# We can't rename ours since the automated ccp4i interface expects it there,
+# as do many scripts. app-office/sc can't rename its because that's the name
+# of the package.
+RDEPEND="X? (
+		x11-libs/libX11
+		x11-libs/libXt
+		x11-libs/libXaw
+		x11-libs/libxdl_view
+		x11-libs/libjwc_c
+		x11-libs/libjwc_f
+		)
+		>=dev-lang/tk-8.3
+		>=dev-tcltk/blt-2.4
+		virtual/lapack
+		virtual/blas
+		=sci-libs/fftw-2*
+		sci-chemistry/pdb-extract
+		sci-chemistry/rasmol
+		app-shells/tcsh
+		dev-python/pyxml
+		dev-libs/libxml2
+		dev-libs/boehm-gc
+		dev-tcltk/iwidgets
+		>=dev-tcltk/tdom-0.8
+		dev-tcltk/tkimg
+		dev-tcltk/tktreectrl
+		dev-tcltk/itcl
+		dev-tcltk/itk
+		sci-libs/ccp4-libs
+		!app-office/sc
+		!media-libs/raptor"
+DEPEND="${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
+
+	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
+
+	# mosflm has its own ebuild
+#	ccp_patch ${FILESDIR}/${PV}-dont-build-mosflm.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 '/^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/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
+
+	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
+
+	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~^\(.*setenv CCP4_BROWSER.*\).*~\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"
+		${S}/include/ccp4.setup*
+
+	# Get rid of S instances
+	# Also the main clipper library is built as libclipper-core, not libclipper
+#	sed -i \
+#		-e "s:${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
+
+	# Fix libdir in all *.la files
+	sed -i \
+		-e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
+		${D}/usr/$(get_libdir)/*.la
+
+	# Library symlinks
+	local LIBNAMES="libjwc_c.so.0.1.1
+			libjwc_f.so.0.1.1
+			libxdl_viewextra.so.0.0.0
+			libxdl_view.so.2.0.0"
+
+	for LIBNAME in ${LIBNAMES}; do
+		library_dosym ${LIBNAME}
+	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 "${D}"/usr/html
+
+	for i in data rnase toxd; do
+		docinto examples/${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
+
+	# 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 ${1}
+}
+
+# Links libname.so, libname.so.major and libname.so.major.minor
+# to libname.so.major.minor.micro
+library_dosym() {
+	local LIBNAME LIBDIR SUFFIX CORE_LIBNAME LIB_MAJOR LIB_MINOR LIB_VERSIONS
+
+	LIBNAME=${1}
+	LIBDIR=${2:-/usr/$(get_libdir)}
+
+	# Tag / on the end of libdir if needed
+	if [[ ${LIBDIR:$((${#LIBDIR}-1)):1} != "/" ]]; then
+		LIBDIR="${LIBDIR}/"
+	fi
+
+	if [[ "${LIBNAME}" != *.so.* ]]; then
+		msg="library_dosym() requires a shared, versioned library as an argument"
+		eerror "$msg"
+		die "$msg"
+	fi
+
+	SUFFIX=${LIBNAME##*so.}
+	CORE_LIBNAME=${LIBNAME%.so.*}
+	CORE_LIBNAME="${CORE_LIBNAME}.so"
+	LIB_MAJOR=${SUFFIX%%.*}
+	LIB_MINOR=${SUFFIX#*.}
+	LIB_MINOR=${SUFFIX%%.*}
+	LIB_VERSIONS="${LIB_MAJOR} ${LIB_MAJOR}.${LIB_MINOR}"
+	for LIB_SUFFIX in .${LIB_MAJOR} ""; do
+		einfo "Calling dosym ${LIBNAME} ${LIBDIR} ${CORE_LIBNAME} ${LIB_SUFFIX}"
+		dosym ${LIBNAME} ${LIBDIR}${CORE_LIBNAME}${LIB_SUFFIX}
+	done
+}
diff --git a/sci-chemistry/ccp4/files/6.1.1-dont-build-double-and-make-bindir.patch b/sci-chemistry/ccp4/files/6.1.1-dont-build-double-and-make-bindir.patch
new file mode 100644
index 000000000..e62ae12ad
--- /dev/null
+++ b/sci-chemistry/ccp4/files/6.1.1-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/files/6.1.1-dont-build-mosflm.patch b/sci-chemistry/ccp4/files/6.1.1-dont-build-mosflm.patch
deleted file mode 100644
index 0e304a6bd..000000000
--- a/sci-chemistry/ccp4/files/6.1.1-dont-build-mosflm.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- ./x-windows/Makefile.in.orig	2008-08-01 14:21:05.000000000 -0700
-+++ ./x-windows/Makefile.in	2008-08-01 14:21:37.000000000 -0700
-@@ -35,7 +35,7 @@
- #
- # all
- #
--all : xdlview libjwc_c libjwc_f rotgen_ hklview xjiffy ipmosflm
-+all : xdlview libjwc_c libjwc_f rotgen_ hklview xjiffy
- #
- # xdl_view
- #
-@@ -161,7 +161,6 @@
- 	$(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir)
- 	cd $(srcdir)/XCCPJIFFY ; $(MAKE) install
- 	cd $(rotgen_dir); $(MAKE) install
--	$(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir)
- #
- # clean
- #
diff --git a/sci-chemistry/ccp4/files/6.1.1-dont-build-rasmol-and-make-bindir.patch b/sci-chemistry/ccp4/files/6.1.1-dont-build-rasmol-and-make-bindir.patch
deleted file mode 100644
index ee192d221..000000000
--- a/sci-chemistry/ccp4/files/6.1.1-dont-build-rasmol-and-make-bindir.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- ccp4-6.0.99e.orig/x-windows/Makefile.in	2008-07-31 10:36:21.000000000 -0700
-+++ ccp4-6.0.99e/x-windows/Makefile.in	2008-07-31 12:25:36.000000000 -0700
-@@ -35,7 +35,7 @@
- #
- # all
- #
--all : xdlview libjwc_c libjwc_f rotgen_ hklview xjiffy rasmol2 ipmosflm
-+all : xdlview libjwc_c libjwc_f rotgen_ hklview xjiffy ipmosflm
- #
- # xdl_view
- #
-@@ -157,9 +157,9 @@
- #
- install_obj = hklview rotgen ipmosflm
- install: all
-+	mkdir -p $(bindir)
- 	$(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir)
- 	cd $(srcdir)/XCCPJIFFY ; $(MAKE) install
--	$(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir)
- 	cd $(rotgen_dir); $(MAKE) install
- 	$(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir)
- #
diff --git a/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/delete/6.0.1-dont-make-dirs-in-configure.patch
index 1420419ff..1420419ff 100644
--- a/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch
+++ b/sci-chemistry/ccp4/files/delete/6.0.1-dont-make-dirs-in-configure.patch
diff --git a/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch b/sci-chemistry/ccp4/files/delete/6.0.1-ppc-double-define-gerror.patch
index a77d9494a..a77d9494a 100644
--- a/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch
+++ b/sci-chemistry/ccp4/files/delete/6.0.1-ppc-double-define-gerror.patch
diff --git a/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/delete/6.0.2-dont-make-dirs-in-configure.patch
index 1420419ff..1420419ff 100644
--- a/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch
+++ b/sci-chemistry/ccp4/files/delete/6.0.2-dont-make-dirs-in-configure.patch
diff --git a/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch b/sci-chemistry/ccp4/files/delete/6.0.2-gcc-4.1.2-idate-fix.patch
index c118cc53b..c118cc53b 100644
--- a/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch
+++ b/sci-chemistry/ccp4/files/delete/6.0.2-gcc-4.1.2-idate-fix.patch
diff --git a/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch b/sci-chemistry/ccp4/files/delete/6.0.2-ppc-double-define-gerror.patch
index a77d9494a..a77d9494a 100644
--- a/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch
+++ b/sci-chemistry/ccp4/files/delete/6.0.2-ppc-double-define-gerror.patch
diff --git a/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch b/sci-chemistry/ccp4/files/delete/ccp4i-default-to-firefox.patch
index 106db895b..106db895b 100644
--- a/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch
+++ b/sci-chemistry/ccp4/files/delete/ccp4i-default-to-firefox.patch
diff --git a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch b/sci-chemistry/ccp4/files/delete/check-blas-lapack-pthread.patch
index 02a2aa6d8..02a2aa6d8 100644
--- a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch
+++ b/sci-chemistry/ccp4/files/delete/check-blas-lapack-pthread.patch
diff --git a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch b/sci-chemistry/ccp4/files/delete/clipper-find-mccp4-includes.patch
index 3bf5a0652..3bf5a0652 100644
--- a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch
+++ b/sci-chemistry/ccp4/files/delete/clipper-find-mccp4-includes.patch
diff --git a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch b/sci-chemistry/ccp4/files/delete/create-mosflm-bindir.patch
index 34d619757..34d619757 100644
--- a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch
+++ b/sci-chemistry/ccp4/files/delete/create-mosflm-bindir.patch
diff --git a/sci-chemistry/ccp4/files/dont-build-rasmol.patch b/sci-chemistry/ccp4/files/delete/dont-build-rasmol.patch
index 8da54fd26..8da54fd26 100644
--- a/sci-chemistry/ccp4/files/dont-build-rasmol.patch
+++ b/sci-chemistry/ccp4/files/delete/dont-build-rasmol.patch
diff --git a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch b/sci-chemistry/ccp4/files/delete/make-ipmosflm-dir.patch
index 7813141b2..7813141b2 100644
--- a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch
+++ b/sci-chemistry/ccp4/files/delete/make-ipmosflm-dir.patch
diff --git a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch b/sci-chemistry/ccp4/files/delete/make-mosflm-cbf-libdir.patch
index ae4b7633b..ae4b7633b 100644
--- a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch
+++ b/sci-chemistry/ccp4/files/delete/make-mosflm-cbf-libdir.patch
diff --git a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch b/sci-chemistry/ccp4/files/delete/make-mosflm-index-libdir.patch
index 97607b689..97607b689 100644
--- a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch
+++ b/sci-chemistry/ccp4/files/delete/make-mosflm-index-libdir.patch
diff --git a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch b/sci-chemistry/ccp4/files/delete/make-mosflm-libdir.patch
index eac1b9f17..eac1b9f17 100644
--- a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch
+++ b/sci-chemistry/ccp4/files/delete/make-mosflm-libdir.patch
diff --git a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch b/sci-chemistry/ccp4/files/delete/pass-clipper-enablevals.patch
index 3e1a8b0e6..3e1a8b0e6 100644
--- a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch
+++ b/sci-chemistry/ccp4/files/delete/pass-clipper-enablevals.patch
diff --git a/sci-libs/Cgraph/Cgraph-2.04.ebuild b/sci-libs/Cgraph/Cgraph-2.04.ebuild
new file mode 100644
index 000000000..32ad27233
--- /dev/null
+++ b/sci-libs/Cgraph/Cgraph-2.04.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit multilib
+
+DESCRIPTION="A set of C functions that generate PostScript for publication quality scientific plots"
+HOMEPAGE="http://neurovision.berkeley.edu/software/A_Cgraph.html"
+SRC_URI="http://neurovision.berkeley.edu/software/${PN}${PV}.tar.gz"
+
+LICENSE="GPL-2"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE=""
+RDEPEND=""
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${PN}"
+
+src_compile() {
+	cd source
+	emake -j1 \
+		INCLUDE_DIR=/usr/include \
+		LIB_DIR=/usr/$(get_libdir) \
+		CC=$(tc-getCC) \
+		ARCHS="" \
+		CCFLAGS="${CFLAGS}" || \
+	die
+}
diff --git a/sci-libs/Cgraph/Manifest b/sci-libs/Cgraph/Manifest
new file mode 100644
index 000000000..e1cfe8a3a
--- /dev/null
+++ b/sci-libs/Cgraph/Manifest
@@ -0,0 +1,3 @@
+DIST Cgraph2.04.tar.gz 198572 RMD160 dbccd69125c93f10b7776c6520d4e8123ab9dfa8 SHA1 5dc9ccb74a30f2ba05dda708706fcc34c00e0c06 SHA256 694559bd85439e72773c63aad461759751472e6afd7853198296416fcf6fe67e
+EBUILD Cgraph-2.04.ebuild 654 RMD160 2eb1cf62d3e7c187c811eb3b866a0478f9cdadb3 SHA1 45e58884c0bb70d4e8ee2cdeeadadc82e3bdb8e2 SHA256 33d30265a9846d749e17742b479323110eaa8a40d7598566fb35725d7e1b9190
+MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-libs/Cgraph/metadata.xml b/sci-libs/Cgraph/metadata.xml
new file mode 100644
index 000000000..efb490d78
--- /dev/null
+++ b/sci-libs/Cgraph/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+  <email>sci@gentoo.org</email>
+</maintainer>
+</pkgmetadata>
diff --git a/sci-libs/chooch/Manifest b/sci-libs/chooch/Manifest
new file mode 100644
index 000000000..0633e2aca
--- /dev/null
+++ b/sci-libs/chooch/Manifest
@@ -0,0 +1,3 @@
+DIST chooch-5.0.2.tar.gz 3057641 RMD160 5eb6d2b33f58e3a0b6379713184cd0c11d3a5956 SHA1 ec6cefd5044487c79e8099329c9f6eb3061e047d SHA256 ad80d5d296bfbd2bb8f9fac930df5a4e9ba583e23b2de298209b7a6925240643
+EBUILD chooch-5.0.2.ebuild 468 RMD160 cf67838d9a356a8c8504db1799c1e14aecad0f02 SHA1 d34ff4b8f4eca7cbbf8e30c0385819cf441fcdb8 SHA256 b6060170d10f297aa4ef398eb6a5c05182329ea1bd03bd09ce2eba808fc79576
+MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-libs/chooch/chooch-5.0.2.ebuild b/sci-libs/chooch/chooch-5.0.2.ebuild
new file mode 100644
index 000000000..c99bc6dc7
--- /dev/null
+++ b/sci-libs/chooch/chooch-5.0.2.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+# inherit
+
+DESCRIPTION="a program that will automatically determine values of the anomalous scattering factors"
+HOMEPAGE="http://www.gwyndafevans.co.uk/id2.html"
+SRC_URI="ftp://ftp.ccp4.ac.uk/chooch/5.0.2/packed/chooch-5.0.2.tar.gz"
+
+LICENSE="ccp4"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="X"
+RDEPEND="X? ( sci-libs/pgplot )
+	 sci-libs/gsl
+	 "
+DEPEND="${RDEPEND}"
+
+
diff --git a/sci-libs/chooch/metadata.xml b/sci-libs/chooch/metadata.xml
new file mode 100644
index 000000000..efb490d78
--- /dev/null
+++ b/sci-libs/chooch/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+  <email>sci@gentoo.org</email>
+</maintainer>
+</pkgmetadata>