re-manifest

116 files changed, 2507 insertions, 859 deletions

diff --git a/patches/ccp4/6.1.2/fix-baubles.patch b/patches/ccp4/6.1.2/fix-baubles.patch
new file mode 100644
index 000000000..2c5f659b8
--- /dev/null
+++ b/patches/ccp4/6.1.2/fix-baubles.patch
@@ -0,0 +1,22 @@
+--- ccp4i/etc/configure.def.dist	2009-01-09 16:45:08.000000000 +0100
++++ ccp4i/etc/configure.def.dist.new	2009-07-07 23:17:26.000000000 +0200
+@@ -53,8 +53,8 @@
+ RUN_IMOSFLM               _text "ccp4iwish [file join [GetEnvPath CCP4I_TOP] imosflm imosflm.tcl] project [GetCurrentProjectDir [GetCurrentProject]]"
+ RUN_CCP4MG                _text                     "ccp4mg"
+ RUN_COOT                  _text                     "coot"
+-RUN_BAUBLES               _text                     "python [file join [GetEnvPath CCP4] share smartie baubles.py]"
+-RUN_DBVIEWER              _text                     "wish [file join [GetEnvPath CCP4] share dbccp4i application viewer.tcl]"
++RUN_BAUBLES               _text                     "python [file join [GetEnvPath CCP4] share ccp4 smartie baubles.py]"
++RUN_DBVIEWER              _text                     "wish [file join [GetEnvPath DBCCP4I_TOP] application viewer.tcl]"
+ ENABLE_BUBBLE_HELP        _logical                  1
+ DISABLE_TASKS             _logical                  1
+ CCP4_SETUP_COMMAND        _text                     setup_ccp4
+@@ -62,7 +62,7 @@
+ BLT_LIBRARY               _text                     ""
+ MENU_LENGTH               _positiveint              25
+ HYPERTEXT_VIEWER          _text                     firefox
+-START_NETSCAPE	          _text			    netscape
++START_NETSCAPE	          _text			    firefox
+ O_MAPMAN                  _text                     mapman
+ MAPMAN_MAXSIZE		  _positiveint		    4194304
+ QUANTA_MBKALL             _text                     mbkall
diff --git a/patches/ccp4/6.1.2/rename-rapper.patch b/patches/ccp4/6.1.2/rename-rapper.patch
new file mode 100644
index 000000000..a50ae6dbd
--- /dev/null
+++ b/patches/ccp4/6.1.2/rename-rapper.patch
@@ -0,0 +1,12 @@
+--- ccp4i/scripts/rapper.script 2009-02-03 11:49:50.000000000 +0100
++++ ccp4i/scripts/rapper.script.new     2009-03-12 23:34:47.000000000 +0100
+@@ -17,7 +17,7 @@
+ 
+ #set up command line 
+ 
+-set cmd "[BinPath rapper]"
++set cmd "[BinPath rappermc]"
+ 
+ set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper]
+ set paramsfile [FileJoin [GetEnvPath CCP4] share rapper params.xml]
+
diff --git a/patches/ccp4/6.1.2/rename-superpose.patch b/patches/ccp4/6.1.2/rename-superpose.patch
new file mode 100644
index 000000000..90480eb8e
--- /dev/null
+++ b/patches/ccp4/6.1.2/rename-superpose.patch
@@ -0,0 +1,12 @@
+diff -arNu ccp4-6.1.1/ccp4i/scripts/superpose.script ccp4-6.1.1.new/ccp4i/scripts/superpose.script
+--- ccp4-6.1.1/ccp4i/scripts/superpose.script	2006-07-26 16:22:49.000000000 +0200
++++ ccp4-6.1.1.new/ccp4i/scripts/superpose.script	2009-07-05 22:11:59.000000000 +0200
+@@ -21,7 +21,7 @@
+ 
+   if { [regexp SSM $SUPERPOSE_MODE ] } {
+ 
+-    set cmd "[BinPath superpose] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\""
++    set cmd "[BinPath superpose-ccp4] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\""
+     set status [Execute $cmd "" program_status report ]
+ 
+   } elseif { [regexp TOP $SUPERPOSE_MODE ] } {
diff --git a/patches/ccp4/6.1.2/rename-truncate.patch b/patches/ccp4/6.1.2/rename-truncate.patch
new file mode 100644
index 000000000..26f1cda3e
--- /dev/null
+++ b/patches/ccp4/6.1.2/rename-truncate.patch
@@ -0,0 +1,22 @@
+--- ./ccp4i/templates/truncate.com.orig	2009-03-02 23:31:04.000000000 -0800
++++ ./ccp4i/templates/truncate.com	2009-03-02 23:31:08.000000000 -0800
+@@ -11,7 +11,7 @@
+ $SYMMETRY symmetry $SPACE_GROUP
+ $CELL cell $CELL_1 $CELL_2 $CELL_3 $CELL_4 $CELL_5 $CELL_6
+ 
+-1 truncate
++1 ftruncate
+  - { [StringSame $APPLY_TRUNCATE "WILSON" ] } YES | NO
+ {[IfSet $ANOMALOUS]} anomalous 
+  - $ANOMALOUS YES | NO
+--- ./ccp4i/scripts/truncate.script.orig	2009-03-02 23:39:04.000000000 -0800
++++ ./ccp4i/scripts/truncate.script	2009-03-02 23:39:41.000000000 -0800
+@@ -45,7 +45,7 @@
+ 
+   CreateComScript truncate truncate_script
+ 
+-  set cmd "[BinPath truncate] HKLIN \"$HKLIN\""
++  set cmd "[BinPath ftruncate] HKLIN \"$HKLIN\""
+   if { ![StringSame $INPUT_DATA AMPLITUDES] } {
+     append cmd " HKLOUT \"$HKL_TRUNCATE\""
+   }
diff --git a/profiles/package.mask b/profiles/package.mask
index 6e4bcbc03..6c9216ecd 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,26 @@
 
 #--- END OF EXAMPLES ---
 
+# Justin Lecher (jlec) (31 Jul 09)
+# jlec@j-schmitz.net
+# to be excluded from ccp4 -- file collision
+=sci-chemistry/scala-3.3.15
+
+# Justin Lecher (jlec) (31 Jul 09)
+# jlec@j-schmitz.net
+# Upcoming release. Upstream still not ready
+=sci-chemistry/ccp4-apps-6.1.2
+
+# Justin Lecher (jlec) (29 Jul 09)
+# jlec@j-schmitz.net
+# Upcoming release. Upstream still not ready
+=sci-chemistry/ccp4i-6.1.2
+
+# Justin Lecher (jlec) (28 Jul 09)
+# jlec@j-schmitz.net
+# Upcoming release. Upstream still not ready
+=sci-libs/ccp4-libs-6.1.2
+
 # Justin Lecher (jlec) (18 Jun 09)
 # jlec@j-schmitz.net
 # Upcoming release. Upstream still not ready
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..f1204695a
--- /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 9837 RMD160 72f50158de5e577927157bd4e908bba709840377 SHA1 f52cfbfdf6b020e318a75954f9dd7260b8e80056 SHA256 8f76f655d60b7a78db5a85889c1e03885e0a8a7326f3d0e613cd35782c1da75c
+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..0487237aa
--- /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"
+
+
+RDEPEND="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>
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=""
diff --git a/sci-chemistry/ccp4i/ChangeLog b/sci-chemistry/ccp4i/ChangeLog
index 096a1df88..37afcdbeb 100644
--- a/sci-chemistry/ccp4i/ChangeLog
+++ b/sci-chemistry/ccp4i/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*ccp4i-6.1.2 (29 Jul 2009)
+
+  29 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/6.1.2-fix-baubles.patch, +ccp4i-6.1.2.ebuild,
+  +files/6.1.2-rename-rapper.patch, +files/6.1.2-rename-superpose.patch,
+  +files/6.1.2-rename-truncate.patch:
+  this is still not released
+
   07 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
   ccp4i-6.1.1-r5.ebuild:
   added media-gfx/graphviz as dep
diff --git a/sci-chemistry/ccp4i/Manifest b/sci-chemistry/ccp4i/Manifest
index ea482fe9e..8937f0786 100644
--- a/sci-chemistry/ccp4i/Manifest
+++ b/sci-chemistry/ccp4i/Manifest
@@ -2,12 +2,18 @@ AUX 6.1.1-fix-baubles.patch 1542 RMD160 c952d16d1e009a9ff345393494bf198fff997934
 AUX 6.1.1-rename-rapper.patch 380 RMD160 e8306cec04348a56fbe00026333b27ce2a8544f8 SHA1 f5a87898394add359a1e6f6ceb837530dc53646f SHA256 e15407959e565d32874d2db9003168559b7e9b14f0e68207560d4a5b4db8a728
 AUX 6.1.1-rename-superpose.patch 655 RMD160 6647dc3e0a021f9809d74d5dd785dd6bde456c22 SHA1 485a2e3cd46864769c6cfe10b9b0224ca896d2d6 SHA256 75791921692a603baa88dfa45ff48331ea8b6985a63f04a15ad43dd5be93e52e
 AUX 6.1.1-rename-truncate.patch 810 RMD160 33f8cb14a3bc0f9c6cd249df07f469c9d6601e4d SHA1 ac13f02b6141802e3762efe50a3d270169da0a54 SHA256 5a298cce47726d78ece397affdf1f2d550be520565c7dc5b47a953ab01d23ccd
+AUX 6.1.2-fix-baubles.patch 1542 RMD160 c952d16d1e009a9ff345393494bf198fff997934 SHA1 cdc8752026f3cdd96ee0fd6a3f558e0729f88a6a SHA256 37c217f339a46a6b830ce8e791cbd32655e31ab8d58267fb625e841e867402b4
+AUX 6.1.2-rename-rapper.patch 380 RMD160 e8306cec04348a56fbe00026333b27ce2a8544f8 SHA1 f5a87898394add359a1e6f6ceb837530dc53646f SHA256 e15407959e565d32874d2db9003168559b7e9b14f0e68207560d4a5b4db8a728
+AUX 6.1.2-rename-superpose.patch 655 RMD160 6647dc3e0a021f9809d74d5dd785dd6bde456c22 SHA1 485a2e3cd46864769c6cfe10b9b0224ca896d2d6 SHA256 75791921692a603baa88dfa45ff48331ea8b6985a63f04a15ad43dd5be93e52e
+AUX 6.1.2-rename-truncate.patch 810 RMD160 33f8cb14a3bc0f9c6cd249df07f469c9d6601e4d SHA1 ac13f02b6141802e3762efe50a3d270169da0a54 SHA256 5a298cce47726d78ece397affdf1f2d550be520565c7dc5b47a953ab01d23ccd
 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 247203373 RMD160 d2ead65da0a2561a8a256cdaa15a6b1a02b6d49e SHA1 fe94461fcafa7074231e01221760e24bb886d605 SHA256 875137beb74cb385b89fe3e49feeda78330c175861a590ee5f7cdbec26bc0e8a
 EBUILD ccp4i-6.1.1-r1.ebuild 1219 RMD160 f2030fb10f766e5de0415e5cbb2edd78da5df5cd SHA1 b6e382f2591c44c1cad007fb7295f397ca464022 SHA256 49c498adffd6e7e3458313754379197c2d20c04a5b63cfcf714595a0bda93d9c
 EBUILD ccp4i-6.1.1-r3.ebuild 1350 RMD160 281c23e4228348c0942f970ec932f4b6d3602c60 SHA1 89d241ee5f11c7bb6222bd3087e5fba610f8b0dc SHA256 bc0e4ca3ca917844680eb9db6a4384e5bf81f02a81b44096d18f4770d462f384
 EBUILD ccp4i-6.1.1-r4.ebuild 1402 RMD160 11a0a5cc10a161de17ae5a89bf7196f5eedd2aab SHA1 a4497b1cb3e422de88e9101942c1f05792b2e361 SHA256 c33033c967364b1ab27957d09aedca70bc852dce8df7d1728c07c8d57c73974a
 EBUILD ccp4i-6.1.1-r5.ebuild 1444 RMD160 c69583b66d51e059ef2ba00c304c7830d32bfebf SHA1 6a590ca81abdb2d41a6131d257595f01e2799da7 SHA256 44a1124ee6797fc66030ce4610655bfd4c74d451add4dd865f9806bde422c19b
-MISC ChangeLog 1698 RMD160 69694b09b7d7e2ed3a8c8fa5efe0ef22cd07dc80 SHA1 92736df6aeec2fb216ce7833eff682c92f070d6a SHA256 4767d1fdcccffb9c87093dbedebbe40f661ef6575e5a0755aef5831af6f5c703
+EBUILD ccp4i-6.1.2.ebuild 1567 RMD160 265130c5a80874772b8c4b0d23cdf7229aa1fc41 SHA1 dbb0d0b1293165037c8fdf90ed8fbd0e78ceb7a1 SHA256 e663d4754eb62fbd506f30511b2849e9c4b945032e1dfeca3523b1ac04f531f1
+MISC ChangeLog 1979 RMD160 535e9ee65921404f090798029f17593c4f2aaa7e SHA1 27a47ca852172e6077497d0d70a837289a31da43 SHA256 cc88d52759064da6650c8dafcd66d7b2e4f939c9acd7775979c429093ab200e4
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-chemistry/ccp4i/ccp4i-6.1.2.ebuild b/sci-chemistry/ccp4i/ccp4i-6.1.2.ebuild
new file mode 100644
index 000000000..da0ed1192
--- /dev/null
+++ b/sci-chemistry/ccp4i/ccp4i-6.1.2.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+inherit multilib base
+
+MY_PN="${PN%i}"
+MY_P="${MY_PN}-${PV}"
+
+#UPDATE="04_03_09"
+#PATCHDATE="090511"
+
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
+
+DESCRIPTION="Protein X-ray crystallography toolkit -- graphical interface"
+HOMEPAGE="http://www.ccp4.ac.uk/"
+SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
+[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
+[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+LICENSE="ccp4"
+IUSE=""
+
+RESTRICT="mirror"
+
+RDEPEND=">=dev-lang/tk-8.3
+	>=dev-tcltk/blt-2.4
+	app-shells/tcsh
+	media-gfx/graphviz"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-rename-truncate.patch
+	"${FILESDIR}"/${PV}-rename-rapper.patch
+	"${FILESDIR}"/${PV}-rename-superpose.patch
+	"${FILESDIR}"/${PV}-fix-baubles.patch
+	)
+
+src_prepare() {
+	base_src_prepare
+
+	sed -i \
+		-e "s:share smartie:share ccp4 smartie:g" \
+		"${S}"/ccp4i/imosflm/src/processingwizard.tcl
+
+	[[ ! -z ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
+}
+
+src_configure() {
+	:
+}
+
+src_compile() {
+	:
+}
+
+src_install() {
+	# CCP4Interface - GUI
+	insinto /usr/$(get_libdir)/ccp4
+	doins -r "${S}"/ccp4i || die
+	exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin
+	doexe "${S}"/ccp4i/bin/* || die
+
+	# dbccp4i
+	insinto /usr/share/ccp4
+	doins -r "${S}"/share/dbccp4i || die
+}
diff --git a/sci-chemistry/ccp4i/files/6.1.2-fix-baubles.patch b/sci-chemistry/ccp4i/files/6.1.2-fix-baubles.patch
new file mode 100644
index 000000000..2c5f659b8
--- /dev/null
+++ b/sci-chemistry/ccp4i/files/6.1.2-fix-baubles.patch
@@ -0,0 +1,22 @@
+--- ccp4i/etc/configure.def.dist	2009-01-09 16:45:08.000000000 +0100
++++ ccp4i/etc/configure.def.dist.new	2009-07-07 23:17:26.000000000 +0200
+@@ -53,8 +53,8 @@
+ RUN_IMOSFLM               _text "ccp4iwish [file join [GetEnvPath CCP4I_TOP] imosflm imosflm.tcl] project [GetCurrentProjectDir [GetCurrentProject]]"
+ RUN_CCP4MG                _text                     "ccp4mg"
+ RUN_COOT                  _text                     "coot"
+-RUN_BAUBLES               _text                     "python [file join [GetEnvPath CCP4] share smartie baubles.py]"
+-RUN_DBVIEWER              _text                     "wish [file join [GetEnvPath CCP4] share dbccp4i application viewer.tcl]"
++RUN_BAUBLES               _text                     "python [file join [GetEnvPath CCP4] share ccp4 smartie baubles.py]"
++RUN_DBVIEWER              _text                     "wish [file join [GetEnvPath DBCCP4I_TOP] application viewer.tcl]"
+ ENABLE_BUBBLE_HELP        _logical                  1
+ DISABLE_TASKS             _logical                  1
+ CCP4_SETUP_COMMAND        _text                     setup_ccp4
+@@ -62,7 +62,7 @@
+ BLT_LIBRARY               _text                     ""
+ MENU_LENGTH               _positiveint              25
+ HYPERTEXT_VIEWER          _text                     firefox
+-START_NETSCAPE	          _text			    netscape
++START_NETSCAPE	          _text			    firefox
+ O_MAPMAN                  _text                     mapman
+ MAPMAN_MAXSIZE		  _positiveint		    4194304
+ QUANTA_MBKALL             _text                     mbkall
diff --git a/sci-chemistry/ccp4i/files/6.1.2-rename-rapper.patch b/sci-chemistry/ccp4i/files/6.1.2-rename-rapper.patch
new file mode 100644
index 000000000..a50ae6dbd
--- /dev/null
+++ b/sci-chemistry/ccp4i/files/6.1.2-rename-rapper.patch
@@ -0,0 +1,12 @@
+--- ccp4i/scripts/rapper.script 2009-02-03 11:49:50.000000000 +0100
++++ ccp4i/scripts/rapper.script.new     2009-03-12 23:34:47.000000000 +0100
+@@ -17,7 +17,7 @@
+ 
+ #set up command line 
+ 
+-set cmd "[BinPath rapper]"
++set cmd "[BinPath rappermc]"
+ 
+ set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper]
+ set paramsfile [FileJoin [GetEnvPath CCP4] share rapper params.xml]
+
diff --git a/sci-chemistry/ccp4i/files/6.1.2-rename-superpose.patch b/sci-chemistry/ccp4i/files/6.1.2-rename-superpose.patch
new file mode 100644
index 000000000..90480eb8e
--- /dev/null
+++ b/sci-chemistry/ccp4i/files/6.1.2-rename-superpose.patch
@@ -0,0 +1,12 @@
+diff -arNu ccp4-6.1.1/ccp4i/scripts/superpose.script ccp4-6.1.1.new/ccp4i/scripts/superpose.script
+--- ccp4-6.1.1/ccp4i/scripts/superpose.script	2006-07-26 16:22:49.000000000 +0200
++++ ccp4-6.1.1.new/ccp4i/scripts/superpose.script	2009-07-05 22:11:59.000000000 +0200
+@@ -21,7 +21,7 @@
+ 
+   if { [regexp SSM $SUPERPOSE_MODE ] } {
+ 
+-    set cmd "[BinPath superpose] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\""
++    set cmd "[BinPath superpose-ccp4] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\""
+     set status [Execute $cmd "" program_status report ]
+ 
+   } elseif { [regexp TOP $SUPERPOSE_MODE ] } {
diff --git a/sci-chemistry/ccp4i/files/6.1.2-rename-truncate.patch b/sci-chemistry/ccp4i/files/6.1.2-rename-truncate.patch
new file mode 100644
index 000000000..26f1cda3e
--- /dev/null
+++ b/sci-chemistry/ccp4i/files/6.1.2-rename-truncate.patch
@@ -0,0 +1,22 @@
+--- ./ccp4i/templates/truncate.com.orig	2009-03-02 23:31:04.000000000 -0800
++++ ./ccp4i/templates/truncate.com	2009-03-02 23:31:08.000000000 -0800
+@@ -11,7 +11,7 @@
+ $SYMMETRY symmetry $SPACE_GROUP
+ $CELL cell $CELL_1 $CELL_2 $CELL_3 $CELL_4 $CELL_5 $CELL_6
+ 
+-1 truncate
++1 ftruncate
+  - { [StringSame $APPLY_TRUNCATE "WILSON" ] } YES | NO
+ {[IfSet $ANOMALOUS]} anomalous 
+  - $ANOMALOUS YES | NO
+--- ./ccp4i/scripts/truncate.script.orig	2009-03-02 23:39:04.000000000 -0800
++++ ./ccp4i/scripts/truncate.script	2009-03-02 23:39:41.000000000 -0800
+@@ -45,7 +45,7 @@
+ 
+   CreateComScript truncate truncate_script
+ 
+-  set cmd "[BinPath truncate] HKLIN \"$HKLIN\""
++  set cmd "[BinPath ftruncate] HKLIN \"$HKLIN\""
+   if { ![StringSame $INPUT_DATA AMPLITUDES] } {
+     append cmd " HKLOUT \"$HKL_TRUNCATE\""
+   }
diff --git a/sci-chemistry/gabedit/ChangeLog b/sci-chemistry/gabedit/ChangeLog
new file mode 100644
index 000000000..9aba62c0a
--- /dev/null
+++ b/sci-chemistry/gabedit/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/gabedit
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*gabedit-2.2.3 (28 Jul 2009)
+
+  28 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +gabedit-2.2.3.ebuild, +metadata.xml:
+  version bump
+
diff --git a/sci-chemistry/gabedit/Manifest b/sci-chemistry/gabedit/Manifest
index 411b014c1..16de45231 100644
--- a/sci-chemistry/gabedit/Manifest
+++ b/sci-chemistry/gabedit/Manifest
@@ -1,2 +1,6 @@
 DIST Gabedit218Src.tar.gz 1452235 RMD160 9fae2509fa439107f61db81dd07659d44b34c90b SHA1 9b31da6bf75e75df89e59cd857deb99fcedae1f3 SHA256 fe7ad6ffbd96164346fba5e8dc6aa24638dcd1e8ba62c5164b8fa60160be9d23
+DIST GabeditSrc223.tar.gz 1625080 RMD160 67eb638a7be343c023690ef025b31f6f88937d2d SHA1 9b72734ef6653df2d4640d3110ffcda4266098b1 SHA256 bf4e3431fabfa7645e10e325ed579c916feaf01978ce3b5db6799e25a17159bd
 EBUILD gabedit-2.1.8.ebuild 965 RMD160 707023c2dbfc94634871792c6395a5bae150a179 SHA1 c4d1cad084437ae5c1feb37549abd8b43d9f585c SHA256 092ba7105282791f719c2d7ea7c960dc90978264e1f96ed8d31725e2599ca493
+EBUILD gabedit-2.2.3.ebuild 1138 RMD160 7a0112fbb9b011a286cf4a2f7f6681b24e89a74d SHA1 9a0f4907690a4f78bbf69daadb8d8b14d5933698 SHA256 d7462644b00416e12895ad89cfc159f8e77b7d9784b6f30e42a1d84a182df3b5
+MISC ChangeLog 265 RMD160 eaba1a87698da00892f31debdc9bec2b76a971dc SHA1 9297ec7fdb984817291af8d5bd5c2b1a08511f6b SHA256 fd34a7eb145ab75508233c10b06fd5852d414925c092fb1573f92aba760b8c63
+MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-chemistry/gabedit/gabedit-2.2.3.ebuild b/sci-chemistry/gabedit/gabedit-2.2.3.ebuild
new file mode 100644
index 000000000..5bde51471
--- /dev/null
+++ b/sci-chemistry/gabedit/gabedit-2.2.3.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=2
+
+inherit toolchain-funcs versionator
+
+MY_PN=${PN/g/G}
+MY_PV=$(delete_all_version_separators)
+MY_P="${MY_PN}Src${MY_PV}"
+
+DESCRIPTION="GUI for computational chemistry packages"
+HOMEPAGE="http://gabedit.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/GabeditDevloppment/${MY_PN}${MY_PV}/${MY_P}.tar.gz"
+#/gabedit/GabeditDevloppment/Gabedit223/GabeditSrc223.tar.gz?use_mirror=dfn
+#/gabedit/GabeditDevloppment/Gabedit223/Gabedit223Src.tar.gz
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+RDEPEND=">=x11-libs/gtk+-2.4
+	x11-libs/gtkglarea
+	x11-libs/gl2ps
+	virtual/opengl
+	virtual/glu"
+DEPEND="${RDEPEND}
+	dev-util/pkgconfig"
+S=${WORKDIR}/${MY_P}
+
+src_prepare() {
+	sed -i \
+		-e "/GTK_DISABLE_DEPRECATED/s:define:undef:g" \
+		"${S}/Config.h" \
+		|| die
+}
+
+src_compile() {
+	emake \
+		CC=$(tc-getCC) \
+		COMMONCFLAGS="${CFLAGS}" \
+		OGLLIB="-lGL -lGLU -lgtkgl-2.0 -lgl2ps" \
+		OGLCFLAGS= \
+		external_gtkglarea=1 \
+		external_gl2ps=1 \
+		|| die
+}
+
+src_install() {
+	dobin ${PN} || die
+	dodoc ChangeLog || die
+}
diff --git a/sci-chemistry/gabedit/metadata.xml b/sci-chemistry/gabedit/metadata.xml
new file mode 100644
index 000000000..efb490d78
--- /dev/null
+++ b/sci-chemistry/gabedit/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-chemistry/molrep/ChangeLog b/sci-chemistry/molrep/ChangeLog
index f662ba0b7..43913ea38 100644
--- a/sci-chemistry/molrep/ChangeLog
+++ b/sci-chemistry/molrep/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*molrep-10.2.33 (29 Jul 2009)
+
+  29 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  -files/10.2.24-respect-FLAGS.patchbak, +molrep-10.2.33.ebuild,
+  +files/10.2.33-respect-FLAGS.patch:
+  version bump
+
 *molrep-10.2.32 (01 Jul 2009)
 
   01 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/molrep/Manifest b/sci-chemistry/molrep/Manifest
index 1b2b7fc03..14aac2809 100644
--- a/sci-chemistry/molrep/Manifest
+++ b/sci-chemistry/molrep/Manifest
@@ -1,9 +1,11 @@
-AUX 10.2.24-respect-FLAGS.patchbak 1729 RMD160 ec37f01a8909a6c1f2ba643aa3e88daa76865226 SHA1 80c01a0b7982fdd62a907309ccfdfa51037136a1 SHA256 cf84b22ba3a48cccb039f53fcd9725952ac6b322919d65230bf60789a16bf40b
 AUX 10.2.27-respect-FLAGS.patch 2376 RMD160 d11071cc402375b2376b6202f960b6f909d1b8df SHA1 7c1ea85188776bbf1054ef18efd55c04343ba187 SHA256 30b55e61663e217c1ee5ef12fe9954046016e303f77f9ff52caa6959c3e3eaa5
 AUX 10.2.32-respect-FLAGS.patch 2368 RMD160 4f24b345f0c78de0c0222abfef987d61fe1356d0 SHA1 bc445d646208de7e879a5989b66296fd89b2fc96 SHA256 809d9f290a1eb59b8fc5904328e72c30b65d3be821a61a1bff050bc446bdc991
+AUX 10.2.33-respect-FLAGS.patch 2368 RMD160 4f24b345f0c78de0c0222abfef987d61fe1356d0 SHA1 bc445d646208de7e879a5989b66296fd89b2fc96 SHA256 809d9f290a1eb59b8fc5904328e72c30b65d3be821a61a1bff050bc446bdc991
 DIST molrep-10.2.27.tar.gz 3595088 RMD160 6e36b6bf992fb306b67de6e483a3487c5fc21da3 SHA1 04d1ecdbd62498703d3c9f3a7d31659074f75c66 SHA256 85c15c827936540134ab65ea9de5a13faa789edeea0f39f65ec1b319ca43c42a
 DIST molrep-10.2.32.tar.gz 3601054 RMD160 bc71b85de92871d540073b1df48e4df7be843a5a SHA1 514a902306bfdb606a4975f95a31859392ff51f7 SHA256 d6736d11cef2638eb4534d65c31871396d3404c8a3011d55bad81fecd810a8b7
+DIST molrep-10.2.33.tar.gz 3601155 RMD160 e0259ddb935c039af27d8ce338341d893da743ad SHA1 37f261ee159342bb9c0487d115265c73aaed295b SHA256 f986aa5653349c692cff522aa6bba3c5b8672251e90d6daf39f10c49539a00ce
 EBUILD molrep-10.2.27.ebuild 1160 RMD160 b1f07fbe73c3b00b494fc18e1b9a267e2c575a3d SHA1 4c134783e6212b7d36a90d8f8237b71bc54ee31e SHA256 81e4901a4e5fb86e1af154de28eac6be0c4c142b4d145a9e4c054ac2b342e15b
 EBUILD molrep-10.2.32.ebuild 1160 RMD160 760335990f17b01524937e009f6841c452cce60b SHA1 fbcb65b2d613ce8e6e2b3e224155ef34c8e938a9 SHA256 d064d9b69c369a810330bad8c1e549649d0c35799082f3f14f2ec93a45389d4a
-MISC ChangeLog 699 RMD160 d1f03022f4649e788f398f7e8780385611fa1883 SHA1 19f059c4e20c3bd4465f9f772d7cb8c0548e8090 SHA256 08322277ba869fd9e294f9da0485a3e292b484f2f1248abf6a27570b49e04886
+EBUILD molrep-10.2.33.ebuild 1160 RMD160 760335990f17b01524937e009f6841c452cce60b SHA1 fbcb65b2d613ce8e6e2b3e224155ef34c8e938a9 SHA256 d064d9b69c369a810330bad8c1e549649d0c35799082f3f14f2ec93a45389d4a
+MISC ChangeLog 906 RMD160 af014fc3f74207f9a300ee38ab04f4460b20e4f9 SHA1 b41c11693f389c22a3f45baf87ce577cceac842a SHA256 100b2461cebffec629cf7e576dfebe3834e09273baf90e3eb2c1a7a1354026a8
 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-chemistry/molrep/files/10.2.24-respect-FLAGS.patchbak b/sci-chemistry/molrep/files/10.2.33-respect-FLAGS.patch
index 89f789ad0..d81ec793b 100644
--- a/sci-chemistry/molrep/files/10.2.24-respect-FLAGS.patchbak
+++ b/sci-chemistry/molrep/files/10.2.33-respect-FLAGS.patch
@@ -1,40 +1,53 @@
 --- src/makefile	2009-02-27 16:51:46.492890717 +0100
 +++ src/makefile.new	2009-02-27 16:52:18.295619642 +0100
+@@ -5,8 +5,8 @@
+ 
+ BIN = $(MOLREP)/bin
+ 
+-OBJS =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym.o molrep_unix.o
+-OBJSL =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym.o molrep_unix.o
++OBJS =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym_ccp4.o molrep_unix_ccp4.o
++OBJSL =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym_ccp4.o molrep_unix_ccp4.o
+ 
+ 
+ all: molrep
 @@ -19,31 +19,31 @@
  # -----------------------------
  
  molrep.o: molrep.f 
 -	$(MR_FORT) -c molrep.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep.f molrep_version.fh
++	$(MR_FORT) $(FFLAGS) -c molrep.f
  molrep1.o: molrep1.f 
 -	$(MR_FORT) -c molrep1.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep1.f mr_crd_com.fh
++	$(MR_FORT) $(FFLAGS) -c molrep1.f
  molrep2.o: molrep2.f 
 -	$(MR_FORT) -c molrep2.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep2.f mr_crd_com.fh
++	$(MR_FORT) $(FFLAGS) -c molrep2.f
  molrep3.o: molrep3.f 
 -	$(MR_FORT) -c molrep3.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep3.f mr_crd_com.fh
++	$(MR_FORT) $(FFLAGS) -c molrep3.f
  molrep_prog.o: molrep_prog.f 
 -	$(MR_FORT) -c molrep_prog.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep_prog.f mr_crd_com.fh mr_crd2_com.fh
++	$(MR_FORT) $(FFLAGS) -c molrep_prog.f
  molrep_prog1.o: molrep_prog1.f 
 -	$(MR_FORT) -c molrep_prog1.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep_prog1.f mr_crd_com.fh
++	$(MR_FORT) $(FFLAGS) -c molrep_prog1.f
  molrep_prog2.o: molrep_prog2.f 
 -	$(MR_FORT) -c molrep_prog2.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep_prog2.f mr_crd_com.fh
++	$(MR_FORT) $(FFLAGS) -c molrep_prog2.f
  molrep_subr.o: molrep_subr.f  
 -	$(MR_FORT) -c molrep_subr.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep_subr.f mr_crd_com.fh mr_crd2_com.fh
- molrep_sym.o: molrep_sym.f  
+-molrep_sym.o: molrep_sym.f  
 -	$(MR_FORT) -c molrep_sym.f 
++	$(MR_FORT) $(FFLAGS) -c molrep_subr.f
++molrep_sym_ccp4.o: molrep_sym.f  
 +	$(MR_FORT) $(FFLAGS) -c molrep_sym_ccp4.f 
  main_molrep_mtz.o: main_molrep_mtz.f molrep_version.fh molrep_keywords.fh 
 -	$(MR_FORT) -c main_molrep_mtz.f 
-+	$(MR_FORT) $(FFLAGS) -c main_molrep_mtz.f 
- molrep_unix.o: molrep_unix.f 
+-molrep_unix.o: molrep_unix.f 
 -	$(MR_FORT) -c molrep_unix.f 
++	$(MR_FORT) $(FFLAGS) -c main_molrep_mtz.f 
++molrep_unix_ccp4.o: molrep_unix.f 
 +	$(MR_FORT) $(FFLAGS) -c molrep_unix_ccp4.f 
  molrep_dummy.o: molrep_dummy.f 
 -	$(MR_FORT) -c molrep_dummy.f 
diff --git a/sci-chemistry/molrep/molrep-10.2.33.ebuild b/sci-chemistry/molrep/molrep-10.2.33.ebuild
new file mode 100644
index 000000000..09be4f2a0
--- /dev/null
+++ b/sci-chemistry/molrep/molrep-10.2.33.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+inherit base multilib toolchain-funcs
+
+DESCRIPTION="molecular replacement program"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html"
+SRC_URI="http://dev.gentooexperimental.org/~jlec/science-dist/${P}.tar.gz"
+
+LICENSE="ccp4"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE=""
+RDEPEND=">=sci-libs/ccp4-libs-6.1.1
+	virtual/lapack"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${PN}"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-respect-FLAGS.patch
+	)
+
+src_compile() {
+	cd "${S}"/src
+	emake \
+		MR_FORT=$(tc-getFC) \
+		FFLAGS="${FFLAGS}" \
+		LDFLAGS="${LDFLAGS}" \
+		MR_LIBRARY="-L/usr/$(get_libdir) -lccp4f -lccp4c -lmmdb -lccif -llapack -lstdc++ -lm" \
+	|| die
+}
+
+src_test() {
+	ewarn "Can take a long, long time ..."
+	ewarn "Go, take a coffee, lunch, go to sleep and have breakfast ..."
+	cd molrep_check && \
+		sed 's:\.\.:\.:g' -i em.bat && \
+		mkdir out && \
+		mkdir scr && \
+		MR_TEST="${S}/bin" bash em.bat && \
+		MR_TEST="${S}/bin" bash mr.bat || \
+		die "test failed"
+}
+
+src_install() {
+	dobin bin/${PN} || die
+
+	dodoc readme doc/${PN}.rtf || die
+}
diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 86657f0fb..ba0467f7c 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,23 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*pymol-1.2.1 (31 Jul 2009)
+*pymol-1.2.0 (31 Jul 2009)
+
+  31 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  -pymol-1.2_rc0.ebuild, -pymol-1.2_rc1.ebuild, 
+  -files/1.2_beta8-nosplash-gentoo.patch, -pymol-1.2_beta8.ebuild, 
+  -pymol-1.2_rc0.ebuild, -pymol-1.2_rc1.ebuild,
+  -files/pymol-1.2_beta8-data-path.patch,
+  +files/pymol-1.2.0-data-path.patch, -files/pymol-1.2_beta8-shaders.patch,
+  -files/pymol-1.2_rc1-data-path.patch, +pymol-1.2.0.ebuild,
+  +files/pymol-1.2.0-shaders.patch, -files/pymol-1.2_rc0-data-path.patch,
+  -files/pymol-1.2_rc1-shaders.patch, +pymol-1.2.1.ebuild,
+  +files/pymol-1.2.1-data-path.patch, -files/pymol-1.2_rc0-shaders.patch,
+  +files/pymol-1.2.1-shaders.patch, -files/apbs-070604-r3550.patch.bz2:
+  mv to correct versions
+  cleanup old uneeded versions
+
   17 Jul 2009; Jeff Gardner <je_fro@gentoo.org> ChangeLog:
   Fix up patch to apply to rc1
 
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 90a67f69a..8d95cd459 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,18 +1,13 @@
-AUX 1.2_beta8-nosplash-gentoo.patch 466 RMD160 2e6afc0b62abc7e8a007c12b887238ece57d323e SHA1 977f2acef4e1a7c30da9dd0510b926ccf56f08c5 SHA256 59fd77f8c7e60e13bb1347c865432574d238a9ce0c705517e291df5880a11768
-AUX apbs-070604-r3550.patch.bz2 20283 RMD160 e7fc42934dea043000ba81e4f27b99b6062e4b12 SHA1 1708de792a53ac4819dfe4ec11cc9ee54b3d5fb9 SHA256 ad8ce064ee2ce3310f862b60b8f762ef713f9952fef0ebd329204a2d25b42db5
 AUX nosplash-gentoo.patch 485 RMD160 3b3d85ffe14a253e54c4ff89b210cf35effe7aee SHA1 627affce7ee9763e308cf6dee70b831e09bd829d SHA256 acf8ef1d53719c1b4158b0f49250e8ed7c3aa4c870ef7ce4bdbc8ec97f591e27
-AUX pymol-1.2_beta8-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8
-AUX pymol-1.2_beta8-shaders.patch 524 RMD160 07d83746617fba941bba8ad95d889e22e5310c9a SHA1 2cbbd82a91029d7c540535c83b0f2663e58a891e SHA256 96b1e2b30c7d6699d87a9efb5cab242db66683f71bfd58bbc69f87ce4df397e0
-AUX pymol-1.2_rc0-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8
-AUX pymol-1.2_rc0-shaders.patch 524 RMD160 07d83746617fba941bba8ad95d889e22e5310c9a SHA1 2cbbd82a91029d7c540535c83b0f2663e58a891e SHA256 96b1e2b30c7d6699d87a9efb5cab242db66683f71bfd58bbc69f87ce4df397e0
-AUX pymol-1.2_rc1-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8
-AUX pymol-1.2_rc1-shaders.patch 442 RMD160 db5ee361cd1e253b9aa012098d08eb7873d95da3 SHA1 881d25514bc744d6f12b5f30bfa1709ed45dba05 SHA256 48042a9baf28c35a55204f646f14eddcf5093e17f518d7de2ffc50cbb7914dda
+AUX pymol-1.2.0-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8
+AUX pymol-1.2.0-shaders.patch 524 RMD160 07d83746617fba941bba8ad95d889e22e5310c9a SHA1 2cbbd82a91029d7c540535c83b0f2663e58a891e SHA256 96b1e2b30c7d6699d87a9efb5cab242db66683f71bfd58bbc69f87ce4df397e0
+AUX pymol-1.2.1-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8
+AUX pymol-1.2.1-shaders.patch 442 RMD160 db5ee361cd1e253b9aa012098d08eb7873d95da3 SHA1 881d25514bc744d6f12b5f30bfa1709ed45dba05 SHA256 48042a9baf28c35a55204f646f14eddcf5093e17f518d7de2ffc50cbb7914dda
 AUX pymol-9999-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8
 AUX pymol-9999-shaders.patch 524 RMD160 07d83746617fba941bba8ad95d889e22e5310c9a SHA1 2cbbd82a91029d7c540535c83b0f2663e58a891e SHA256 96b1e2b30c7d6699d87a9efb5cab242db66683f71bfd58bbc69f87ce4df397e0
 DIST apbs_tools.py.090618.bz2 21329 RMD160 80baed718524dfbaff2f0a3b7263fc75c55bf1d9 SHA1 e2c69bb150679f137ba7ff2cfcd0fe2da000612b SHA256 604803ed58f1827b76cbf5f3b58c35859d31c68d51481da4b37e08a1c0656d6e
-EBUILD pymol-1.2_beta8.ebuild 2707 RMD160 8329ceb3b22bbebe66e62d6bb5f78e39edd9ce22 SHA1 062f9887da79aa83325463ae350e290a275dfef4 SHA256 efa34926bd8545b707728c05184b1a5cf8c2bbd2bcd796439577e5e996fe7c4a
-EBUILD pymol-1.2_rc0.ebuild 2726 RMD160 e4fbf3696379427d95b88e1631748c0a7ef2deff SHA1 d79acbbc0a5a8602330c3735cdc7311ff3a94f77 SHA256 4a97a8c7da7056d19a9a1ab8ec58b5311b6868d5267c793fc9e6b782d6f9f5e0
-EBUILD pymol-1.2_rc1.ebuild 2726 RMD160 cc3392e76e4ba82a886e1bf2925e4cabdc7a4a63 SHA1 afada6e399c2d405fc9741d9dcb7abe1ec04bf0d SHA256 741949fedda03f738b248fe34f504b65cd59de734a660d5b2c6b1bdf8902607d
+EBUILD pymol-1.2.0.ebuild 2726 RMD160 e4fbf3696379427d95b88e1631748c0a7ef2deff SHA1 d79acbbc0a5a8602330c3735cdc7311ff3a94f77 SHA256 4a97a8c7da7056d19a9a1ab8ec58b5311b6868d5267c793fc9e6b782d6f9f5e0
+EBUILD pymol-1.2.1.ebuild 2726 RMD160 cc3392e76e4ba82a886e1bf2925e4cabdc7a4a63 SHA1 afada6e399c2d405fc9741d9dcb7abe1ec04bf0d SHA256 741949fedda03f738b248fe34f504b65cd59de734a660d5b2c6b1bdf8902607d
 EBUILD pymol-9999.ebuild 2981 RMD160 1d609dd649eadf68293340adb19c3b05b206e5f5 SHA1 b161cc3344f98660cb18e7a97621cf311c297d5f SHA256 3b315033850b04249d94a211b0c5105fcd76f1b938688a44f2e9a274d808f3f9
-MISC ChangeLog 4664 RMD160 28887c1bb0f6c7f0943072c752209081b3352117 SHA1 f7bb690593a580b11d2c7dfff6284cf1838a4623 SHA256 d05dde7827ea9786b30f414b2b7c4d6a422cb737794b55d92182a43ab6e5c330
+MISC ChangeLog 5456 RMD160 15cfbbbb68320ea9d3c173e2ae2867c387cbd15b SHA1 48139fc4a56532234beb57d4f8eac1be2afc40c0 SHA256 d2cb7186c17f1d035358bc8a182d8c78ef885eaf74c28d07688659a6451ac88b
 MISC metadata.xml 412 RMD160 9c33c90cdb3bc60af7dbee004b7f1cffd1b43aa6 SHA1 efd4a32d739fe54f0f464edc0843c81e9fb23437 SHA256 ee0056aa8c9e40b6da007fa8c895e15c17cb25004212b91d48dad03f6123483c
diff --git a/sci-chemistry/pymol/files/1.2_beta8-nosplash-gentoo.patch b/sci-chemistry/pymol/files/1.2_beta8-nosplash-gentoo.patch
deleted file mode 100644
index 18f228524..000000000
--- a/sci-chemistry/pymol/files/1.2_beta8-nosplash-gentoo.patch
+++ /dev/null
@@ -1,9 +0,0 @@
---- modules/pymol/invocation.py	2009-06-30 14:27:39.000000000 +0200
-+++ modules/pymol/invocation.py.new	2009-06-30 14:30:01.000000000 +0200
-@@ -372,6 +372,4 @@
-         if loaded_something and (options.after_load_script!=""):
-             options.deferred.append(options.after_load_script)
-         options.deferred.extend(final_actions)
--        if options.show_splash and not options.no_gui:
--            options.deferred.insert(0,"_do__ cmd.splash(1)")
-         
diff --git a/sci-chemistry/pymol/files/apbs-070604-r3550.patch.bz2 b/sci-chemistry/pymol/files/apbs-070604-r3550.patch.bz2
deleted file mode 100644
index 396a4d26d..000000000
--- a/sci-chemistry/pymol/files/apbs-070604-r3550.patch.bz2
+++ /dev/null
diff --git a/sci-chemistry/pymol/files/pymol-1.2_beta8-data-path.patch b/sci-chemistry/pymol/files/pymol-1.2.0-data-path.patch
index 86c3fe1f1..86c3fe1f1 100644
--- a/sci-chemistry/pymol/files/pymol-1.2_beta8-data-path.patch
+++ b/sci-chemistry/pymol/files/pymol-1.2.0-data-path.patch
diff --git a/sci-chemistry/pymol/files/pymol-1.2_beta8-shaders.patch b/sci-chemistry/pymol/files/pymol-1.2.0-shaders.patch
index 7f4a24f48..7f4a24f48 100644
--- a/sci-chemistry/pymol/files/pymol-1.2_beta8-shaders.patch
+++ b/sci-chemistry/pymol/files/pymol-1.2.0-shaders.patch
diff --git a/sci-chemistry/pymol/files/pymol-1.2_rc0-data-path.patch b/sci-chemistry/pymol/files/pymol-1.2.1-data-path.patch
index 86c3fe1f1..86c3fe1f1 100644
--- a/sci-chemistry/pymol/files/pymol-1.2_rc0-data-path.patch
+++ b/sci-chemistry/pymol/files/pymol-1.2.1-data-path.patch
diff --git a/sci-chemistry/pymol/files/pymol-1.2_rc1-shaders.patch b/sci-chemistry/pymol/files/pymol-1.2.1-shaders.patch
index 06f756823..06f756823 100644
--- a/sci-chemistry/pymol/files/pymol-1.2_rc1-shaders.patch
+++ b/sci-chemistry/pymol/files/pymol-1.2.1-shaders.patch
diff --git a/sci-chemistry/pymol/files/pymol-1.2_rc0-shaders.patch b/sci-chemistry/pymol/files/pymol-1.2_rc0-shaders.patch
deleted file mode 100644
index 7f4a24f48..000000000
--- a/sci-chemistry/pymol/files/pymol-1.2_rc0-shaders.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-diff -uarN pymol-9999.orig/setup.py pymol-9999/setup.py
---- pymol-9999.orig/setup.py	2008-06-18 11:47:58.000000000 +0200
-+++ pymol-9999/setup.py	2008-06-18 11:48:52.000000000 +0200
-@@ -143,6 +143,7 @@
-     def_macros=[("_PYMOL_MODULE",None),
-                     ("_PYMOL_INLINE",None),
-                     ("_PYMOL_FREETYPE",None),
-+                    ("_PYMOL_OPENGL_SHADERS",None),
- # Numeric Python support                    
- #                        ("_PYMOL_NUMPY",None),
- # VMD plugin support                    
diff --git a/sci-chemistry/pymol/files/pymol-1.2_rc1-data-path.patch b/sci-chemistry/pymol/files/pymol-1.2_rc1-data-path.patch
deleted file mode 100644
index 86c3fe1f1..000000000
--- a/sci-chemistry/pymol/files/pymol-1.2_rc1-data-path.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff -arNu -uarN pymol/modules/pymol/commanding.py pymol.new/modules/pymol/commanding.py
---- pymol/modules/pymol/commanding.py	2009-03-31 12:43:14.585834066 +0200
-+++ pymol.new/modules/pymol/commanding.py	2009-03-31 12:44:26.436354330 +0200
-@@ -219,11 +219,11 @@
-                 _self.unlock(0,_self)
-             r = DEFAULT_SUCCESS
-             if show_splash==1: # generic / open-source
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/splash.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/splash.png")
-             elif show_splash==2: # evaluation builds
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/epymol.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/epymol.png")
-             else: # incentive builds
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/ipymol.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/ipymol.png")
-             if os.path.exists(png_path):
-                 _self.do("_ cmd.load_png('%s',0,quiet=1)"%png_path)
-         else:
-diff -arNu -uarN pymol/modules/pymol/importing.py pymol.new/modules/pymol/importing.py
---- pymol/modules/pymol/importing.py	2009-03-31 12:43:14.546250540 +0200
-+++ pymol.new/modules/pymol/importing.py	2009-03-31 12:44:48.876657949 +0200
-@@ -191,7 +191,7 @@
-     '''
-         r = DEFAULT_ERROR
-         
--        tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png",
-+        tables = { 'cmyk' : "$PYMOL_DATA/pymol/cmyk.png",
-                    'pymol' : 'pymol',
-                    'rgb' : 'rgb' }
-         
diff --git a/sci-chemistry/pymol/pymol-1.2_rc0.ebuild b/sci-chemistry/pymol/pymol-1.2.0.ebuild
index 5b872e771..5b872e771 100644
--- a/sci-chemistry/pymol/pymol-1.2_rc0.ebuild
+++ b/sci-chemistry/pymol/pymol-1.2.0.ebuild
diff --git a/sci-chemistry/pymol/pymol-1.2_rc1.ebuild b/sci-chemistry/pymol/pymol-1.2.1.ebuild
index 60eb583ee..60eb583ee 100644
--- a/sci-chemistry/pymol/pymol-1.2_rc1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.2.1.ebuild
diff --git a/sci-chemistry/pymol/pymol-1.2_beta8.ebuild b/sci-chemistry/pymol/pymol-1.2_beta8.ebuild
deleted file mode 100644
index 1ff55eb49..000000000
--- a/sci-chemistry/pymol/pymol-1.2_beta8.ebuild
+++ /dev/null
@@ -1,114 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-PYTHON_MODNAME="chempy pmg_tk pymol"
-APBS_PATCH="090618"
-REV="3761"
-
-inherit distutils subversion
-
-ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol@${REV}"
-
-DESCRIPTION="A Python-extensible molecular graphics system."
-HOMEPAGE="http://pymol.sourceforge.net/"
-SRC_URI="apbs? ( http://dev.gentooexperimental.org/~jlec/distfiles/apbs_tools.py.${APBS_PATCH}.bz2 )"
-
-LICENSE="PSF-2.2"
-IUSE="apbs shaders"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-python/pmw
-		dev-python/numpy
-		>=dev-lang/python-2.4[tk]
-		media-libs/libpng
-		sys-libs/zlib
-		virtual/glut
-		apbs? ( dev-libs/maloc
-				sci-chemistry/apbs
-				sci-chemistry/pdb2pqr
-		)"
-DEPEND="${RDEPEND}"
-
-pkg_setup(){
-	python_version
-}
-
-src_unpack() {
-	use apbs && unpack ${A}
-	subversion_src_unpack
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-data-path.patch || die
-
-	# Turn off splash screen.  Please do make a project contribution
-	# if you are able though.
-	[[ -n ${WANT_SPLASH} ]] || epatch "${FILESDIR}"/${PV}-nosplash-gentoo.patch
-
-	# Respect CFLAGS
-	sed -i \
-		-e "s:\(ext_comp_args=\).*:\1[]:g" \
-		"${S}"/setup.py
-
-	use shaders && epatch "${FILESDIR}"/${P}-shaders.patch
-
-	if use apbs; then
-		cp -f "${WORKDIR}"/apbs_tools.py.${APBS_PATCH} modules/pmg_tk/startup/apbs_tools.py || die
-		sed "s:LIBANDPYTHON:$(python_get_libdir):g" \
-			-i modules/pmg_tk/startup/apbs_tools.py || die
-	fi
-}
-
-src_configure() {
-	:
-}
-
-src_install() {
-	distutils_src_install
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH=$(python_get_sitedir)/${PN}
-		PYMOL_DATA="/usr/share/pymol/data"
-		PYMOL_SCRIPTS="/usr/share/pymol/scripts"
-	EOF
-
-	use apbs && \
-	echo "APBS_PSIZE=$(python_get_sitedir)/pdb2pqr/src/psize.py" >> "${T}"/20pymol
-
-	doenvd "${T}"/20pymol || die "Failed to install env.d file."
-
-	cat >> "${T}"/pymol <<- EOF
-	#!/bin/sh
-	${python} -O \${PYMOL_PATH}/__init__.py \$*
-	EOF
-
-	dobin "${T}"/pymol || die "Failed to install wrapper."
-
-	insinto /usr/share/pymol
-	doins -r test data scripts || die "no shared data"
-
-	insinto /usr/share/pymol/examples
-	doins -r examples || die "Failed to install docs."
-
-	dodoc DEVELOPERS README || die "Failed to install docs."
-
-	if ! use apbs; then
-		rm "${D}"$(python_get_sitedir)/pmg_tk/startup/apbs_tools.py
-	fi
-}
-
-pkg_postinst(){
-	distutils_pkg_postinst
-
-	# The apbs ebuild was just corrected and not bumped #213616
-	if use apbs; then
-		[ -e /usr/share/apbs-0.5* ] && \
-		ewarn "You need to reemerge sci-chemistry/apbs!"
-	fi
-}
diff --git a/sci-chemistry/scala/ChangeLog b/sci-chemistry/scala/ChangeLog
new file mode 100644
index 000000000..d0f4ee0dd
--- /dev/null
+++ b/sci-chemistry/scala/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-chemistry/scala
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*scala-3.3.15 (31 Jul 2009)
+
+  31 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +scala-3.3.15.ebuild, +files/Makefile.am, +files/configure.ac,
+  +metadata.xml:
+  Initial addition
+  scala will be dropped from ccp4-apps package
+
diff --git a/sci-chemistry/scala/Manifest b/sci-chemistry/scala/Manifest
new file mode 100644
index 000000000..fe4726923
--- /dev/null
+++ b/sci-chemistry/scala/Manifest
@@ -0,0 +1,6 @@
+AUX Makefile.am 73 RMD160 919c14040b76627428d143027260e9ef2deb2836 SHA1 090d67b6052b322bcc8224b4052bfc9aaf9b0743 SHA256 9b964ac556e8343f4ed45d7293d0144aef569d565141a96a555416aeb411feae
+AUX configure.ac 313 RMD160 098fbafb1f83c2925ff2580c5e0191263b37f574 SHA1 e1550b1b27c967660f7d47c62dea9e693983eca4 SHA256 5c54a92c67fc74f1e4700f53aa9962a0315ec3fb2578c1c13694bfb16d3100ff
+DIST scala-3.3.15.tar.gz 366768 RMD160 65dc000ab41f727291b598e77917ef60bf8fd676 SHA1 a86de4d5c8e490359041bc3dacb8dc874ef648ce SHA256 47ab466689f89e923fd8821076c1e2f81f00c7d08403b23f0921e37522f5cc98
+EBUILD scala-3.3.15.ebuild 655 RMD160 6ffe518bfd821909447ab95d3bb0b605bcd74055 SHA1 d26fa2dc83bab38d2523163b8827d6c2fcc278c2 SHA256 8cb6d7db07abb59a271f9e2f672c37ea068bbf23bf6f288ea2da0ef346719b53
+MISC ChangeLog 355 RMD160 64b2f2020cb60ebef4f6620c31ab1867e5502a8f SHA1 d5d4113fb7abecccb0b3b615c6a5dc3d04890915 SHA256 023e55a02ee839c967023e6324a219edc4736924dac9ab4f76ac97d104e46f9e
+MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-chemistry/scala/files/Makefile.am b/sci-chemistry/scala/files/Makefile.am
new file mode 100644
index 000000000..b16394b88
--- /dev/null
+++ b/sci-chemistry/scala/files/Makefile.am
@@ -0,0 +1,7 @@
+
+LIBS = -lccp4f -llapack
+
+bin_PROGRAMS = scala
+
+scala_SOURCES = scala.f
+
diff --git a/sci-chemistry/scala/files/configure.ac b/sci-chemistry/scala/files/configure.ac
new file mode 100644
index 000000000..bcbd7dede
--- /dev/null
+++ b/sci-chemistry/scala/files/configure.ac
@@ -0,0 +1,12 @@
+#                                               -*- Autoconf -*-
+# Process this file with autoconf to produce a configure script.
+
+AC_PREREQ(2.59)
+AC_INIT(scala, https://bugs.gentoo.org/)
+AC_CONFIG_SRCDIR([scala.f])
+AM_INIT_AUTOMAKE([foreign])
+
+# Checks for programs.
+AC_PROG_FC
+AC_PROG_F77
+AC_OUTPUT([Makefile])
diff --git a/sci-chemistry/scala/metadata.xml b/sci-chemistry/scala/metadata.xml
new file mode 100644
index 000000000..efb490d78
--- /dev/null
+++ b/sci-chemistry/scala/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-chemistry/scala/scala-3.3.15.ebuild b/sci-chemistry/scala/scala-3.3.15.ebuild
new file mode 100644
index 000000000..350db654e
--- /dev/null
+++ b/sci-chemistry/scala/scala-3.3.15.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+inherit autotools fortran
+
+FORTRAN="gfortran ifc"
+
+DESCRIPTION="scale together multiple observations of reflections"
+HOMEPAGE="http://www.ccp4.ac.uk/dist/html/scala.html"
+SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz"
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="sci-libs/ccp4-libs
+	virtual/lapack"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	cp "${FILESDIR}"/{configure.ac,Makefile.am} "${S}"
+	eautoreconf
+}
+
+src_install() {
+	dobin ${PN} || die
+	dodoc ${PN}.txt || die
+	dohtml ${PN}.html || die
+}
diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest
index d1e0331d8..d9fdee297 100644
--- a/sci-chemistry/tinker/Manifest
+++ b/sci-chemistry/tinker/Manifest
@@ -1,4 +1,4 @@
 DIST tinker.tar.gz 8177555 RMD160 95f904f03f6a1767bbf73b00f326d19a164b7a1c SHA1 b42c5763958869894ee91fcd2ed4c5e03d8c1e5d SHA256 ad0cc9782dabdb0cce490fe26508761a36078e741f019090cbaa3e6cacf71055
-EBUILD tinker-5.0.ebuild 1845 RMD160 9099d5e35f26521a1daced4e2c420d749f51cb14 SHA1 aa2953ee8745008a6a999687b49603e09ca8904b SHA256 22c6bb14b4a9b2992ac690afea8b0f251aabd52a809bbb210d570c72ff999e97
+EBUILD tinker-5.0.ebuild 1839 RMD160 5ed51cb45f2322fa8e81e2d2d8da9f9183e0821e SHA1 bcb155641ea804350cac8d6f85ac2c840d8128c7 SHA256 4f90d84cca19a948e84b4086cc063f5ec2c3273d0acaefb9523bb2c1fe8a8e4a
 MISC ChangeLog 2370 RMD160 8b5d727c2720d348f6f00ff0846c505b71746e27 SHA1 f34a340ee01f2a597b8e17acc2f2da39c9d85dcb SHA256 5395df8360f6dd6700e0bc1c8957a5f42c663be966c6319c6e86e7f8bf1a88b0
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-chemistry/tinker/tinker-5.0.ebuild b/sci-chemistry/tinker/tinker-5.0.ebuild
index 84f989021..a6ba12f6e 100644
--- a/sci-chemistry/tinker/tinker-5.0.ebuild
+++ b/sci-chemistry/tinker/tinker-5.0.ebuild
@@ -27,17 +27,17 @@ src_compile() {
 	if [[ ${FORTRANC} == "ifc" ]]; then
 		cp ../linux/intel/* .
 	else
-		cp ../linux/gfortran/* .
+		cp ../linux/gnu/* .
 	fi
 
 	cp ../make/* .
 
 	# Prep build scripts
-	sed -i -e "s:gfortran:${FORTRANC} ${LDFLAGS}:g" ${LINK}
+	sed -i -e "s:g77:${FORTRANC} ${LDFLAGS}:g" ${LINK}
 
 	# Default to -O2 if FFLAGS is unset
-	sed -i -e "s:-O:${FFLAGS:- -O2}:" ${COMPILE}
-	sed -i -e "s:gfortran:${FORTRANC}:g" ${COMPILE}
+	sed -i -e "s:-O3 -ffast-math:${FFLAGS:- -O2}:" ${COMPILE}
+	sed -i -e "s:g77:${FORTRANC}:g" ${COMPILE}
 
 	einfo "Compiling ..."
 	${COMPILE} || die "compile failed"
@@ -48,25 +48,24 @@ src_compile() {
 }
 
 src_install() {
-	exeinto /usr/bin
-
 	dodoc \
 		"${WORKDIR}"/tinker/doc/*.txt \
 		"${WORKDIR}"/tinker/doc/release-${PV} \
 		"${WORKDIR}"/tinker/doc/*.pdf
 
-	dolib.a libtinker.a
+	dolib.a libtinker.a || die
 
 	for EXE in *.x; do
-		newexe ${EXE} ${EXE%.x}
+		newbin ${EXE} ${EXE%.x} || die
 	done
 
 	docinto example
 	dodoc "${WORKDIR}"/tinker/example/*
+
 	docinto test
 	dodoc "${WORKDIR}"/tinker/test/*
 
-	doexe "${WORKDIR}"/tinker/perl/mdavg
+	dobin "${WORKDIR}"/tinker/perl/mdavg
 
 	insinto /usr/share/tinker/params
 	doins "${WORKDIR}"/tinker/params/*
diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog
index c7ec65515..3f9143c2d 100644
--- a/sci-libs/ccp4-libs/ChangeLog
+++ b/sci-libs/ccp4-libs/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*ccp4-libs-6.1.2 (29 Jul 2009)
+
+  29 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +ccp4-libs-6.1.2.ebuild, +ccp4-libs-6.1.2.ebuild.save,
+  +files/6.1.2-dont-make-dirs-in-configure.patch,
+  +files/6.1.2-glibc2.10.patch, +files/6.1.2-link-proberly.patch:
+  Still not released 6.1.2
+
 *ccp4-libs-6.1.1-r7 (05 Jul 2009)
 
   05 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
index 57a9b23cf..cb1c1a313 100644
--- a/sci-libs/ccp4-libs/Manifest
+++ b/sci-libs/ccp4-libs/Manifest
@@ -2,13 +2,19 @@ AUX 6.0.2-ppc-double-define-gerror.patch 424 RMD160 4f012233446fffa61e8d775a19a0
 AUX 6.1.1-dont-make-dirs-in-configure.patch 2866 RMD160 ba49e45ab609a42a2d93b96f55af913bf9625610 SHA1 36c9329c3768c08687ef062c9ab649d32833b422 SHA256 1b5997f17526a4fd60ffa9eccf4b765aadf3a78c9394657000e0454f364240ca
 AUX 6.1.1-glibc2.10.patch 1018 RMD160 577ee4a6174df36bb8bac82738523f5c757df4b9 SHA1 48ad6d0d024c43d64277e4decba420d51e75a510 SHA256 d2a2ddf2a66738d94723b50797e279f64c8e057a3e584e33f9eb9c8d7ea0e532
 AUX 6.1.1-link-proberly.patch 9325 RMD160 0457062deb5d71f7419d134e89d3d99989fc12b7 SHA1 c7c0453b82b85ae22ea42b562dd2d4ac95b134e7 SHA256 81c4eda497ffa3a0f2d757b7c6b3f6cc35a06ced18ebede2faa31f18667ea8b7
+AUX 6.1.2-dont-make-dirs-in-configure.patch 2866 RMD160 ba49e45ab609a42a2d93b96f55af913bf9625610 SHA1 36c9329c3768c08687ef062c9ab649d32833b422 SHA256 1b5997f17526a4fd60ffa9eccf4b765aadf3a78c9394657000e0454f364240ca
+AUX 6.1.2-glibc2.10.patch 1018 RMD160 577ee4a6174df36bb8bac82738523f5c757df4b9 SHA1 48ad6d0d024c43d64277e4decba420d51e75a510 SHA256 d2a2ddf2a66738d94723b50797e279f64c8e057a3e584e33f9eb9c8d7ea0e532
+AUX 6.1.2-link-proberly.patch 9325 RMD160 0457062deb5d71f7419d134e89d3d99989fc12b7 SHA1 c7c0453b82b85ae22ea42b562dd2d4ac95b134e7 SHA256 81c4eda497ffa3a0f2d757b7c6b3f6cc35a06ced18ebede2faa31f18667ea8b7
 AUX pass-clipper-enablevals.patch 501 RMD160 23466922268a91570b0f64cf79809b988e32689b SHA1 c254d31fe88ed1716a53bd549cf7aee537ca5204 SHA256 d476c9f231fb6cdfb5e57004b393644a88016318cdeed9c33c32de25e0d91b79
 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 247203373 RMD160 d2ead65da0a2561a8a256cdaa15a6b1a02b6d49e SHA1 fe94461fcafa7074231e01221760e24bb886d605 SHA256 875137beb74cb385b89fe3e49feeda78330c175861a590ee5f7cdbec26bc0e8a
 EBUILD ccp4-libs-6.1.1-r4.ebuild 5776 RMD160 3a36e4a2fff69e2a17028c39f8849a4cfd73c64e SHA1 7693f8aa4a3e6106876e68fcdf25fada3b2e61e5 SHA256 f541ab2ffa172978b11c91c11754be4c75bb63174e2c3a4a1990f7e8fa5ddd57
 EBUILD ccp4-libs-6.1.1-r6.ebuild 5956 RMD160 88f4d6e5c9067225501f214002bc5924bc07c1a2 SHA1 8e61890578007833d8a923eeada3bdf064354056 SHA256 1e7bde2c6f9319d699cf95565aa74bd26372b9d1275fdeaaa8ee75fb4001b30a
 EBUILD ccp4-libs-6.1.1-r7.ebuild 6093 RMD160 99176fde51fd41e7b29610a15720859e97b22d01 SHA1 6a52cfb8e4cddd9454db90bb90bad600c3b753ec SHA256 2143d0c1a7905107b9699cce41d7f33a6fedc99cf9046de33d7b42ddafdfa937
 EBUILD ccp4-libs-6.1.1.ebuild 5211 RMD160 6f3705f7ab0c48bbda073eb7dc1a283b3dcaa39a SHA1 8b09909daae034fc393b49b5fda7e06a783bcd14 SHA256 e9b4a3183a8f753ced59968b261bb655c87d13ade8c9964c71f1f2948c42067e
-MISC ChangeLog 2141 RMD160 6a857cfba2a1fe8fb1c6b9a3e3c2c9e84da043aa SHA1 d0a90b7bff5a7afb45df107d20a4a2fe863509e0 SHA256 112b8a324770dd0b672315868749f265a7c684f4e3ac5185bcdf74763bad9393
+EBUILD ccp4-libs-6.1.2.ebuild 6784 RMD160 785dc7bf1ca755b66ab6dad2d2e2a3efc0bfa76d SHA1 b6df87140bb72012ca88920c6ba9f36d5a50c033 SHA256 0cc19814e23e525bb74acc921f22c0c73f9fee522a5bf323259477e0a87c454c
+MISC ChangeLog 2431 RMD160 35e051f578142a24e0c488bb79972b6ec03e8f53 SHA1 51c7326eaee4b4cec3d1f847ba92087ada731263 SHA256 df369e675d208c704403dd341ceb4ef57fb8a0e27760762cc59e6e4bce294d98
+MISC ccp4-libs-6.1.2.ebuild.save 6779 RMD160 b63cef13d5584d4318abfc2db3144c3e844316b0 SHA1 b3d2d68c38b8f4a57607d7010e5b6d9646cba1cc SHA256 b6078ff2f676f0538d3d0ed9bb260d9d5eacd98a95ee3e9f1997f845f53eb40a
 MISC metadata.xml 309 RMD160 b9d7f0a63f8fb51e9b4e2d6b4f4028541df5400c SHA1 26ee4b64e0e4d52b1afe00957d53b0cc2956da00 SHA256 04f156de856eae11c0cf8af213f74a9852213844cdd5133aa01dbe60371d57e7
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild
new file mode 100644
index 000000000..59d82e597
--- /dev/null
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild
@@ -0,0 +1,221 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit fortran eutils gnuconfig toolchain-funcs
+
+FORTRAN="g77 gfortran ifc"
+
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
+
+#UPDATE="04_03_09"
+#PATCHDATE="090511"
+
+MY_P="${P/-libs}"
+
+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"
+#	${SRC}/${PV}/updates/${MY_P}-src-patch-${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/${!NAME}"
+done
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+RDEPEND="virtual/lapack
+	virtual/blas
+	=sci-libs/fftw-2*
+	app-shells/tcsh
+	!<sci-chemistry/ccp4-6.0.99
+	sci-libs/monomer-db"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${P/-libs}"
+
+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}"/${PV}-dont-make-dirs-in-configure.patch
+
+	# gerror_ gets defined twice on ppc if you're using gfortran/g95
+	ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
+
+	einfo "Done." # done applying Gentoo patches
+	echo
+
+	# glibc-2.10 getline fix
+#	sed -e "s:getline:${PN/-libs}getline:g" -i lib/src/fsplit.c || die
+#	ccp_patch "${FILESDIR}"/${PV}-glibc2.10.patch
+
+	gnuconfig_update
+}
+
+src_compile() {
+	# Build system is broken if we set LDFLAGS
+	userldflags="${LDFLAGS}"
+	export SHARED_LIB_FLAGS="${LDFLAGS}"
+	unset LDFLAGS
+
+	# GENTOO_OSNAME can be one of:
+	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
+	# linux_compaq_compilers linux_intel_compilers generic Darwin
+	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
+	if [[ "${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}
+#	export CCP4_SCR="${T}"
+
+	# Fix linking
+	export SHARE_LIB="\
+		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
+		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -lm $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
+		${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -lstdc++ -lgfortran $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
+#	export SHARE_LIB="\
+#		ld -shared -soname libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
+#		ld -shared -soname libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -lm $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
+#		ld -shared -soname libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -lstdc++ -lgfortran $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
+
+	# Can't use econf, configure rejects unknown options like --prefix
+	./configure \
+		--onlylibs \
+		--with-shared-libs \
+		--with-fftw=/usr \
+		--with-warnings \
+		--disable-cctbx \
+		--disable-clipper \
+		--tmpdir="${TMPDIR}" \
+		${GENTOO_OSNAME} || die "econf failed"
+	emake -j1 onlylib || die "emake failed"
+}
+
+src_install() {
+	# Set up variables for build
+	source "${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/$(get_libdir) /usr/bin
+
+#	make install || die "install failed"
+	einstall || die "install failed"
+
+	# Libs
+	for file in "${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
+
+	# Bins
+	dobin bin/{automask,diff2jpeg,diffdump,printpeaks} || die
+	newbin bin/superpose superpose-ccp4 || die
+
+	# Fix libdir in all *.la files
+	sed -i \
+		-e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
+		"${D}"/usr/$(get_libdir)/*.la
+
+	# Data
+	insinto /usr/share/ccp4/data/
+	doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
+	dodoc "${S}"/lib/data/*.doc
+	newdoc "${S}"/lib/data/README DATA-README
+
+	# Include files
+	insinto /usr/include
+	for i in ccp4 mmdb; do
+		doins -r "${S}"/include/${i} || die
+	done
+}
+
+# Epatch wrapper for bulk patching
+ccp_patch() {
+	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
+}
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild.save b/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild.save
new file mode 100644
index 000000000..7cc458e59
--- /dev/null
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild.save
@@ -0,0 +1,221 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit fortran eutils gnuconfig toolchain-funcs
+
+FORTRAN="g77 gfortran ifc"
+
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
+
+#UPDATE="04_03_09"
+#PATCHDATE="090511"
+
+MY_P="${P/-libs}"
+
+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"
+#	${SRC}/${PV}/updates/${MY_P}-src-patch-${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/${!NAME}"
+done
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+RDEPEND="virtual/lapack
+	virtual/blas
+	=sci-libs/fftw-2*
+	app-shells/tcsh
+	!<sci-chemistry/ccp4-6.0.99
+	sci-libs/monomer-db"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${P/-libs}"
+
+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}"/${PV}-dont-make-dirs-in-configure.patch
+
+	# gerror_ gets defined twice on ppc if you're using gfortran/g95
+	ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
+
+	einfo "Done." # done applying Gentoo patches
+	echo
+
+	# glibc-2.10 getline fix
+#	sed -e "s:getline:${PN/-libs}getline:g" -i lib/src/fsplit.c || die
+#	ccp_patch "${FILESDIR}"/${PV}-glibc2.10.patch
+
+	gnuconfig_update
+}
+
+src_compile() {
+	# Build system is broken if we set LDFLAGS
+	userldflags="${LDFLAGS}"
+	export SHARED_LIB_FLAGS="${LDFLAGS}"
+	unset LDFLAGS
+
+	# GENTOO_OSNAME can be one of:
+	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
+	# linux_compaq_compilers linux_intel_compilers generic Darwin
+	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
+	if [[ "${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}
+#	export CCP4_SCR="${T}"
+
+	# Fix linking
+	export SHARE_LIB="\
+		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
+		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -lm $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
+		${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -lstdc++ -lgfortran $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
+#	export SHARE_LIB="\
+#		ld -shared -soname libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
+#		ld -shared -soname libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -lm $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
+#		ld -shared -soname libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -lstdc++ -lgfortran $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
+
+	# Can't use econf, configure rejects unknown options like --prefix
+	./configure \
+		--onlylibs \
+		--with-shared-libs \
+		--with-fftw=/usr \
+		--with-warnings \
+		--disable-cctbx \
+		--disable-clipper \
+		--tmpdir="${TMPDIR}" \
+		${GENTOO_OSNAME} || die "econf failed"
+	emake -j1 onlylib || die "emake failed"
+}
+
+src_install() {
+	# Set up variables for build
+	source "${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/$(get_libdir) /usr/bin
+
+#	make install || die "install failed"
+	einstall || die "install failed"
+
+	# Libs
+	for file in "${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
+
+	# Bins
+	dobin bin/{automask,diff2jpeg,diffdump,printpeaks} || die
+	newbin bin/superpose superpose-ccp4 || die
+
+	# Fix libdir in all *.la files
+	sed -i \
+		-e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
+		"${D}"/usr/$(get_libdir)/*.la
+
+	# Data
+	insinto /usr/share/ccp4/data/
+	doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
+	dodoc "${S}"/lib/data/*.doc
+	newdoc "${S}"/lib/data/README DATA-README
+
+	# Include files
+	insinto /usr/include
+	for i in ccp4 mmdb; do
+		doins -r "${S}"/include/${i} || die
+	done
+}
+
+# Epatch wrapper for bulk patching
+ccp_patch() {
+	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
+}
diff --git a/sci-libs/ccp4-libs/files/6.1.2-dont-make-dirs-in-configure.patch b/sci-libs/ccp4-libs/files/6.1.2-dont-make-dirs-in-configure.patch
new file mode 100644
index 000000000..583697cea
--- /dev/null
+++ b/sci-libs/ccp4-libs/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 $i/Makefile.in
++#       fi
++#     fi
++#   done
++#fi
+ 
+ ### sanity checks
+ 
diff --git a/sci-libs/ccp4-libs/files/6.1.2-glibc2.10.patch b/sci-libs/ccp4-libs/files/6.1.2-glibc2.10.patch
new file mode 100644
index 000000000..6e3997647
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.2-glibc2.10.patch
@@ -0,0 +1,22 @@
+--- lib/ccif/configure.in	2009-06-10 13:52:59.000000000 +0200
++++ lib/ccif/configure.in.new	2009-06-10 14:04:31.000000000 +0200
+@@ -363,7 +363,7 @@
+          fi
+          SHARED_LIB_CMD='$(LD) $(SHARED_LIB_FLAGS) -shared -soname $(SHARED_LIB_NAME) \\\
+                         --whole-archive '"$SHARED_LIB_RESTRICT"' $L \\\
+-                        $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
++                        $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
+          SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
+       fi
+    ;;
+--- lib/ccif/configure	2009-06-10 14:26:58.000000000 +0200
++++ lib/ccif/configure.new	2009-06-10 14:43:31.000000000 +0200
+@@ -1807,7 +1807,7 @@
+          SHARED_LIB_CMD='$(LD) $(SHARED_LIB_CFLAGS) -shared -soname \\\
+ 				$(SHARED_LIB_NAME) \\\
+                                --whole-archive $L \\\
+-                               -o $(SHARED_LIB_NAME)'
++                               -o $(SHARED_LIB_NAME) -lm'
+          SHARED_LIB_EXPORTS_CMD=''
+       fi
+    ;;
diff --git a/sci-libs/ccp4-libs/files/6.1.2-link-proberly.patch b/sci-libs/ccp4-libs/files/6.1.2-link-proberly.patch
new file mode 100644
index 000000000..0780314f0
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.2-link-proberly.patch
@@ -0,0 +1,255 @@
+--- lib/src/Makefile.in	2009-03-02 17:53:15.000000000 +0100
++++ lib/src/Makefile.in.new	2009-03-02 17:52:09.000000000 +0100
+@@ -172,9 +172,8 @@
+ 
+ ##### Makefile targets ######
+ 
+-all:  fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
++all:  fsplit $(LMMDB) LMMDB_SO $(LC) LC_SO $(LF) LF_SO $(SCRIPT_MODULES)
+ # maybe create shared library
+-	$(SHARE_LIB)
+ 
+ $(LC) : $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS)
+ 	$(AR) $(LC) $?
+@@ -186,6 +185,27 @@
+ 	$(AR) $(LF) $(FINTERFACEOBJS)
+ 	$(RANLIB) $@
+ 
++LMMDB_SO : 
++	$(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o libmmdb.so.0.0.0 \
++	$(MMDBOBJS) && \
++	ln -sf libmmdb.so.0.0.0 libmmdb.so.0 && \
++	ln -sf libmmdb.so.0.0.0 libmmdb.so
++
++LC_SO : 
++	$(CC) $(COPTIM) -shared -Wl,-soname,libccp4c.so.0 -o libccp4c.so.0.0.0 \
++	$(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
++	ln -sf libccp4c.so.0.0.0 libccp4c.so.0 && \
++	ln -sf libccp4c.so.0.0.0 libccp4c.so
++
++LF_SO : 
++	$(FC) $(FOPTIM) -shared -Wl,-soname,libccp4f.so.0 -o libccp4f.so.0.0.0 \
++	parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
++	libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
++	harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
++	modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
++	ln -sf libccp4f.so.0.0.0 libccp4f.so.0 && \
++	ln -sf libccp4f.so.0.0.0 libccp4f.so
++
+#@@ -186,6 +185,27 @@
+# 	$(AR) $(LF) $(FINTERFACEOBJS)
+# 	$(RANLIB) $@
+# 
+#+LMMDB_SO : 
+#+	$(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o ../libmmdb.so.0.0.0 \
+#+	$(MMDBOBJS) && \
+#+	ln -sf libmmdb.so.0.0.0 ../libmmdb.so.0 && \
+#+	ln -sf libmmdb.so.0.0.0 ../libmmdb.so
+#+
+#+LC_SO : 
+#+	$(CC) $(COPTIM) -shared -Wl,-soname,libccp4_c.so.0 -o ../libccp4_c.so.0.0.0 \
+#+	$(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
+#+	ln -sf libccp4_c.so.0.0.0 ../libccp4_c.so.0 && \
+#+	ln -sf libccp4_c.so.0.0.0 ../libccp4_c.so
+#+
+#+LF_SO : 
+#+	$(FC) $(FOPTIM) -shared -Wl,-soname,libccp4_f.so.0 -o ../libccp4_f.so.0.0.0 \
+#+	parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
+#+	libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
+#+	harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
+#+	modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
+#+	ln -sf libccp4_f.so.0.0.0 ../libccp4_f.so.0 && \
+#+	ln -sf libccp4_f.so.0.0.0 ../libccp4_f.so
+#+
+ # cmtz library only
+ 
+ cmtz: $(LCMTZ)
+@@ -339,9 +356,7 @@
+ 	fi
+ 	cd parser.dir && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f parser.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ parser : parser.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -351,9 +366,7 @@
+ 	echo '      END' >> ccplib.dir/ccplib.$F
+ 	cd ccplib.dir && $(fsplit_dir)/fsplit $(srcdir)/ccplib.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f ccplib.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ ccplib : ccplib.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -364,9 +377,7 @@
+ 	@$(SETFLAGS) ; \
+ 	cd lgglib.dir && $(fsplit_dir)/fsplit $(srcdir)/lgglib.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    eval $(FC) -c  $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f lgglib.dir/*.o
++	    eval $(FC) -c  $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done
+ lgglib : lgglib.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -376,9 +387,7 @@
+ 	echo '      END' >> plot84lib.dir/plot84lib.$F
+ 	cd plot84lib.dir && $(fsplit_dir)/fsplit $(srcdir)/plot84lib.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f plot84lib.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ plot84lib : plot84lib.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -388,9 +397,7 @@
+ 	echo '      END' >> libhtml.dir/libhtml.$F
+ 	cd libhtml.dir && $(fsplit_dir)/fsplit $(srcdir)/libhtml.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f libhtml.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ libhtml : libhtml.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -400,9 +407,7 @@
+ 	echo '      END' >> pxxml.dir/pxxml.$F
+ 	cd pxxml.dir && $(fsplit_dir)/fsplit $(srcdir)/pxxml.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f pxxml.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ pxxml : pxxml.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -412,9 +417,7 @@
+ 	echo '      END' >> rwbrook.dir/rwbrook.$F
+ 	cd rwbrook.dir && $(fsplit_dir)/fsplit $(srcdir)/rwbrook.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f rwbrook.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ rwbrook : rwbrook.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -424,9 +427,7 @@
+ 	echo '      END' >> cciflib.dir/cciflib.$F
+ 	cd cciflib.dir && $(fsplit_dir)/fsplit $(srcdir)/cciflib.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f cciflib.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done
+ cciflib : cciflib.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -440,9 +441,7 @@
+ 	  && $(AR) ../$(LF) *.o ; else \
+ 	cd harvlib.dir && $(fsplit_dir)/fsplit $(srcdir)/harv_dummy.f >/dev/null && $(RMEMPTY) && \
+ 	for i in `pwd`/*.$F; do \
+-	  $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
+-	  && $(AR) ../$(LF) *.o ; fi
+-	rm -f harvlib.dir/*.o
++	  $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done; fi
+ harvlib : harvlib.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -452,9 +451,7 @@
+ 	echo '      END' >> keyparse.dir/keyparse.$F
+ 	cd keyparse.dir && $(fsplit_dir)/fsplit $(srcdir)/keyparse.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f keyparse.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ keyparse : keyparse.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -464,9 +461,7 @@
+ 	echo '      END' >> dna_output.dir/dna_output.$F
+ 	cd dna_output.dir && $(fsplit_dir)/fsplit $(srcdir)/dna_output.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f dna_output.dir/*.o
++	    $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ dna_output : dna_output.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -474,10 +469,9 @@
+ #  for ipdisp. May be useful but could be moved. 
+ $(LF)(pack_c.o):   $(srcdir)/pack_c.c $(srcdir)/pack_c.h
+ 	$(CC) $(CFLAGS) $(SHARED_LIB_CFLAGS) -I$(srcdir) -c $(srcdir)/pack_c.c
+-	$(AR) $(LF) pack_c.o && rm pack_c.o
++	$(AR) $(LF) pack_c.o
+ $(LF)(pack_f.o):   $(srcdir)/pack_f.f
+-	$(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o \
+-          && rm pack_f.o
++	$(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o
+ pack:   $(LF)(pack_c.o) $(LF)(pack_f.o)
+ 	$(RANLIB) $(LF) 
+ 
+@@ -488,9 +482,7 @@
+ 	echo '      END' >> sorting_main.dir/sorting_main.$F
+ 	cd sorting_main.dir && $(fsplit_dir)/fsplit $(srcdir)/sorting_main.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f sorting_main.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ sorting_main : sorting_main.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -500,9 +492,7 @@
+ 	echo '      END' >> plotsubs.dir/plotsubs.$F
+ 	cd plotsubs.dir && $(fsplit_dir)/fsplit $(srcdir)/plotsubs.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f plotsubs.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ plotsubs : plotsubs.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -512,9 +502,7 @@
+ 	echo '      END' >> modlib.dir/modlib.$F
+ 	cd modlib.dir && $(fsplit_dir)/fsplit $(srcdir)/modlib.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f modlib.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ modlib : modlib.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -524,9 +512,7 @@
+ 	echo '      END' >> fftlib.dir/fftlib.$F
+ 	cd fftlib.dir && $(fsplit_dir)/fsplit $(srcdir)/fftlib.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done \
+-	  && $(AR) ../$(LF) *.o
+-	rm -f fftlib.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done 
+ fftlib : fftlib.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -541,9 +527,7 @@
+ 	echo '      END' >> unix.dir/unix.f
+ 	cd unix.dir && $(fsplit_dir)/fsplit ../unix.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f unix.dir/*.o 
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ unix : unix.o
+ 	$(RANLIB) $(LF)
+ 
diff --git a/sci-libs/monomer-db/ChangeLog b/sci-libs/monomer-db/ChangeLog
index 2768eac35..c757dba78 100644
--- a/sci-libs/monomer-db/ChangeLog
+++ b/sci-libs/monomer-db/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*monomer-db-0.090729 (29 Jul 2009)
+
+  29 Jul 2009; <jlec@gentoo.org> -monomer-db-0.090623.ebuild,
+  +monomer-db-0.090729.ebuild:
+  automatic bump
+
   25 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
   monomer-db-5.13.ebuild:
   version 5.13 fix of installation
diff --git a/sci-libs/monomer-db/Manifest b/sci-libs/monomer-db/Manifest
index 33d7e4bb6..b3c42af60 100644
--- a/sci-libs/monomer-db/Manifest
+++ b/sci-libs/monomer-db/Manifest
@@ -1,6 +1,6 @@
-DIST monomer-db-0.090623.tar.gz 3129184 RMD160 cebaf0d8bc43dd221bf0c77fcf6d694ca65d479c SHA1 5f53124156c7fb0da59496dc2f484039a4fc9728 SHA256 55898355c57be44c7117f91d03fbaa6be116137e49ba236b80b13eec62876d4b
+DIST monomer-db-0.090729.tar.gz 3129184 RMD160 cebaf0d8bc43dd221bf0c77fcf6d694ca65d479c SHA1 5f53124156c7fb0da59496dc2f484039a4fc9728 SHA256 55898355c57be44c7117f91d03fbaa6be116137e49ba236b80b13eec62876d4b
 DIST refmac_dictionary_v5.13.tar.gz 21739189 RMD160 7eceb21a6f22d118d8318ea409eb341cdec637b6 SHA1 7c9d8f261e8842c7c50a228a9c793c5a1fa726a0 SHA256 0513f5f2471db56bccda8d50ecc46305984c774f21b1c6d0b46cc411ec5a68e5
-EBUILD monomer-db-0.090623.ebuild 766 RMD160 4f0a43e0fd1819e390f77c3af18af82d50268928 SHA1 dbcd0b2d1c5836c5266f5520dc04d48c49a4d5d5 SHA256 3f8dfb10f6689c35d9befdb0156bf94002ec3c0682bd5fb72c679206f729c6d0
+EBUILD monomer-db-0.090729.ebuild 766 RMD160 4f0a43e0fd1819e390f77c3af18af82d50268928 SHA1 dbcd0b2d1c5836c5266f5520dc04d48c49a4d5d5 SHA256 3f8dfb10f6689c35d9befdb0156bf94002ec3c0682bd5fb72c679206f729c6d0
 EBUILD monomer-db-5.13.ebuild 754 RMD160 bc061210512cf9a0cfbbe0ec957dabf44e286a47 SHA1 475be4c957aa646c9b3d8e6467c910a0a8d2be14 SHA256 dab71f323bdfbadc5f4220fc53e3a01f8121a20cf1aa6f78c35f2a81aad20091
-MISC ChangeLog 1226 RMD160 ab3e38263a45ccdf3bd274ae57019665572ac12d SHA1 042dc4cd6ef944ee72a8542ed9ed7bff913610e0 SHA256 c6e1d0165cf096e706f5d6e9e41bceb59042d03da83e08fe504ea7c1621b2b0d
+MISC ChangeLog 1373 RMD160 9705d831e4aa64ce6766c849f3572412aeb5e5f4 SHA1 31316ce04fe592fce387e85dbbc1e3fcf5626482 SHA256 da341e9ec3b8e47bb3c79a5fa853d0f87b50011f8097bd82d7961f2992743203
 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-libs/monomer-db/monomer-db-0.090623.ebuild b/sci-libs/monomer-db/monomer-db-0.090729.ebuild
index ab4e0e760..ab4e0e760 100644
--- a/sci-libs/monomer-db/monomer-db-0.090623.ebuild
+++ b/sci-libs/monomer-db/monomer-db-0.090729.ebuild
diff --git a/sci-libs/starparse/ChangeLog b/sci-libs/starparse/ChangeLog
new file mode 100644
index 000000000..148b0b2bf
--- /dev/null
+++ b/sci-libs/starparse/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for sci-libs/starparse
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*starparse-9999 (31 Jul 2009)
+*starparse-9999_pre10 (31 Jul 2009)
+
+  31 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +starparse-9999_pre10.ebuild, +starparse-9999.ebuild, 
+  +metadata.xml:
+  sci-libs/starparse moved from dberkholz overlay to sci
+  bzr.eclass changes fixed
+
diff --git a/sci-libs/starparse/Manifest b/sci-libs/starparse/Manifest
new file mode 100644
index 000000000..2766f4af7
--- /dev/null
+++ b/sci-libs/starparse/Manifest
@@ -0,0 +1,4 @@
+EBUILD starparse-9999.ebuild 695 RMD160 ce0c4e203ae1c6cce9cfd3fe1b01427ba825df7c SHA1 bd9c673c9a96156cd3e7b24ef3b341ae6bbf2402 SHA256 9cd8f0c95418b5765b734ea537c6134c609efebe805a0fdbd88761836ec2e1a3
+EBUILD starparse-9999_pre10.ebuild 757 RMD160 e0fda4ee7a1d5b5e6874f9ecee8d04bfb97d5046 SHA1 2e4868259d64d165d839d8fef782e402d2348279 SHA256 a77dc9a4f35e66d8c7ab7fdca43a882e3e3e876c4e667dccf62691690956d0ec
+MISC ChangeLog 402 RMD160 25147fd28b93e13559de419338392d41e5eda1b1 SHA1 950d99c7666d33b4e19f402f6291764224685dc6 SHA256 81210d617cabc6bd3c893cbadb4e8274d1e4a23b0321cbb6c3015f1aa6c867b8
+MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-libs/starparse/metadata.xml b/sci-libs/starparse/metadata.xml
new file mode 100644
index 000000000..efb490d78
--- /dev/null
+++ b/sci-libs/starparse/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/starparse/starparse-9999.ebuild b/sci-libs/starparse/starparse-9999.ebuild
new file mode 100644
index 000000000..4b754097e
--- /dev/null
+++ b/sci-libs/starparse/starparse-9999.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EBZR_REPO_URI="http://oregonstate.edu/~benisong/software/projects/starparse/head"
+EBZR_BOOTSTRAP="eautoreconf"
+
+inherit autotools bzr
+
+DESCRIPTION="Library for parsing NMR star files (peak-list format) and CIF files"
+HOMEPAGE="http://burrow-owl.sourceforge.net/"
+#SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="guile"
+RDEPEND="guile? ( dev-scheme/guile )"
+DEPEND="${RDEPEND}"
+
+src_compile() {
+	econf $(use_enable guile) || die
+	emake || die
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die "emake install failed"
+}
diff --git a/sci-libs/starparse/starparse-9999_pre10.ebuild b/sci-libs/starparse/starparse-9999_pre10.ebuild
new file mode 100644
index 000000000..1e6c830b1
--- /dev/null
+++ b/sci-libs/starparse/starparse-9999_pre10.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+if [[ ${PV} = 9999* ]]; then
+	EBZR_REPO_URI="http://oregonstate.edu/~benisong/software/projects/starparse/releases/1.0"
+	EBZR_BOOTSTRAP="eautoreconf"
+	BZR="bzr"
+else
+	SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+fi
+
+inherit autotools ${BZR}
+
+DESCRIPTION="Library for parsing NMR star files (peak-list format) and CIF files"
+HOMEPAGE="http://burrow-owl.sourceforge.net/"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="guile"
+
+RDEPEND="guile? ( dev-scheme/guile )"
+DEPEND="${RDEPEND}"
+
+src_compile() {
+	econf $(use_enable guile) || die
+	emake || die
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die "emake install failed"
+}
diff --git a/scripts/update-monomers-db b/scripts/update-monomers-db
index d34c4baea..28e30333c 100644
--- a/scripts/update-monomers-db
+++ b/scripts/update-monomers-db
@@ -34,7 +34,7 @@ cd ${TMPDIR};
 
 wget http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_dictionary.tar.gz
 
-SHA_NEW=$(sha256sum refmac_dictionary.tar.gz)
+SHA_NEW=$(sha256sum refmac_dictionary.tar.gz|awk '{print $1}')
 SHA_OLD=$(sed -n -e '/^DIST monomer/p' ${REPO_DOC}/../sci-libs/monomer-db/Manifest | \
 	tail -n 1 | awk '{print $9}')
 
@@ -42,5 +42,7 @@ if [[ ${SHA_OLD} == ${SHA_NEW} ]]; then
 	echo "Nothing to update"
 else
 	echo "bumping to monomer-db-${DATE} ..."
-	bump_package
+#	bump_package
+	echo ${SHA_OLD}
+	echo ${SHA_NEW} 
 fi
diff --git a/sys-infiniband/dapl/Manifest b/sys-infiniband/dapl/Manifest
index 4ea522f21..ed7a37623 100644
--- a/sys-infiniband/dapl/Manifest
+++ b/sys-infiniband/dapl/Manifest
@@ -1,15 +1,5 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 AUX dapl.conf.2.0.9 700 RMD160 ca541699d8e6ce169ebc7e46aa73cca258c665f9 SHA1 2d8c9c6ee20345f96910b4a1aba49b545defd64b SHA256 9829545c3373ef08df934f5ebb8038b2f0fe75343c24338d1780be0b8771ef2d
 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee
-EBUILD dapl-2.0.15.ebuild 483 RMD160 6b64840e253131b3de4ce227b01d564f858d57ee SHA1 960dea94565d2f272eae9279813a40dcda6ef98f SHA256 930d15cbd16fb37844bb2dc5c1b94c1b7c4771b827c6a78d15880f492c20882a
+EBUILD dapl-2.0.15.ebuild 492 RMD160 a75008a6539a8a1cecc926c20e3c9410345692d9 SHA1 5a1e26fe56d3fd877962c9d5546d0c45ae9cb509 SHA256 ebb4abe8927c270c25daff5256bdb05b801794a099d5ef65b0c7dfa950520de8
 MISC ChangeLog 822 RMD160 65bc0eadc872ec713cb4bb775e65dff93537a520 SHA1 5ce2530a51d512e2abfa9a6e1de4e06bbe48571a SHA256 775886a6f26c81bd59ea3ef5f1538f0f68571d1c20cc23a4e43edbd167dbc00c
 MISC metadata.xml 500 RMD160 0725131b4e5467ff909fe7ef29779969cc007e9f SHA1 06109c0df587604ce753e48cf5c50d0a68d49d05 SHA256 f2dc519f3eb35e8ec665cdca569c649fbf0e24285d1979050dc69318f1350f84
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.10 (GNU/Linux)
-
-iEYEARECAAYFAknC038ACgkQ5BmOA85PVLg6FwCeMrUdrXLf7lL1/xrpkbz4IU1R
-XyoAoKffhAU/kTR1bRZ/U20QuiQkmspl
-=8wps
------END PGP SIGNATURE-----
diff --git a/sys-infiniband/dapl/dapl-2.0.15.ebuild b/sys-infiniband/dapl/dapl-2.0.15.ebuild
index fd5eabd77..0147bbd6b 100644
--- a/sys-infiniband/dapl/dapl-2.0.15.ebuild
+++ b/sys-infiniband/dapl/dapl-2.0.15.ebuild
@@ -13,10 +13,10 @@ DESCRIPTION="OpenIB - Direct Access Provider Library"
 KEYWORDS="~x86 ~amd64"
 IUSE=""
 
-DEPEND=">=sys-cluster/libibverbs-1.1.2
-		>=sys-cluster/librdmacm-1.0.8"
+DEPEND=">=sys-infiniband/libibverbs-1.1.2
+		>=sys-infiniband/librdmacm-1.0.8"
 RDEPEND="${DEPEND}
-		!sys-cluster/openib-userspace"
+		!sys-infiniband/openib-userspace"
 
 src_install() {
 	make DESTDIR="${D}" install || die "install failed"
diff --git a/sys-infiniband/libehca/Manifest b/sys-infiniband/libehca/Manifest
index 987725012..2586cc7cb 100644
--- a/sys-infiniband/libehca/Manifest
+++ b/sys-infiniband/libehca/Manifest
@@ -1,14 +1,4 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee
-EBUILD libehca-1.2.1.ebuild 483 RMD160 d9fb4d6d124079142d507ef650e770065a74e5be SHA1 5fb6ba9e40ac5eaaf50222f066f3b64f59db2d19 SHA256 71769a70fd9734dc0d31e375ea2df853e81814babb7cd24e9bbad6ba21a19ebd
+EBUILD libehca-1.2.1.ebuild 486 RMD160 7f1618e05198c315029c9a9547afa378b1ecec79 SHA1 cc8b25d444ff3b460ed764971e63be9431ab8bc2 SHA256 bde87d3efc0ee572560a02721453c0ffc20a51181d3a910c0e2c1c594b27325c
 MISC ChangeLog 562 RMD160 83b1ee7ac896e78a5b8efb1e58479213e0ac966c SHA1 b824f4382daf4198539a10f75a3dd990a9805b34 SHA256 568edef7f8aba09b493927876ae79c810c276dc382a97c1041f7f2111798b369
 MISC metadata.xml 268 RMD160 b9ad624fa453134e7070265231890b5834717483 SHA1 093332fd523364fdfed959f2ed828b59e92db471 SHA256 375ee8b5598c7090139d3c272fb75276ee2f9cecd2c87e08b667914de8f69693
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.10 (GNU/Linux)
-
-iEYEARECAAYFAknC04QACgkQ5BmOA85PVLi/yACeJDVjGhwSyCNI76SqSHLRAb/k
-VnMAnj8aKFfAxUbfpY0B1tw8SoNxXy/i
-=8GpV
------END PGP SIGNATURE-----
diff --git a/sys-infiniband/libehca/libehca-1.2.1.ebuild b/sys-infiniband/libehca/libehca-1.2.1.ebuild
index e3e8ac33d..dd9c1ec79 100644
--- a/sys-infiniband/libehca/libehca-1.2.1.ebuild
+++ b/sys-infiniband/libehca/libehca-1.2.1.ebuild
@@ -16,7 +16,7 @@ DESCRIPTION="OpenIB - IBM eServer eHCA Infiniband device driver for Linux on POW
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND=">=sys-cluster/libibverbs-1.1.2"
+DEPEND=">=sys-infiniband/libibverbs-1.1.2"
 RDEPEND="${DEPEND}"
 
 src_install() {
diff --git a/sys-infiniband/libibcm/Manifest b/sys-infiniband/libibcm/Manifest
index bd23fcf7c..007e0eea5 100644
--- a/sys-infiniband/libibcm/Manifest
+++ b/sys-infiniband/libibcm/Manifest
@@ -1,14 +1,4 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee
-EBUILD libibcm-1.0.4.ebuild 451 RMD160 02a2e560381b2deb5b6f38f2fe93858541b11d16 SHA1 fd2ebc3b91f26f9de11295d495bff7c43d22b08b SHA256 f25463e978f0c4dba92477a74ac5d53ec159633cecff18930829ddd929144da0
+EBUILD libibcm-1.0.4.ebuild 454 RMD160 0c9d6b71aca23ce18179e64b8702a25b3df446ac SHA1 141467fe511a076153212d12d780d5be6f0a389e SHA256 ace561c1cb5632b5997093fa24a02e7105da349ec4b5c395d1dd953ffbf75290
 MISC ChangeLog 782 RMD160 9b40f9c33ff923741b155ec51065a36ac21b5ebc SHA1 a5237a9aa0afc8b47834cc9877f8bd1e31a0909c SHA256 251a4ed3e205d36e61a26ae49e9e89ce216c321f0da66fc29668c438d3cfbb00
 MISC metadata.xml 225 RMD160 b67ae9b3dfb94a62234aa189d57ce40e5c46b0b0 SHA1 96710bdc512030840adf0958a5409afb6d9a8474 SHA256 f967801055d7bdf11aa1a121654a256cd74c3c5699302138a9120963b3960dac
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.10 (GNU/Linux)
-
-iEYEARECAAYFAknC04kACgkQ5BmOA85PVLgJPQCcCK2yoV5Ge9P/HSNuxBTb1CkT
-7wgAoK296e/pAXZIMp/IjSVylfl28rC3
-=Ggm1
------END PGP SIGNATURE-----
diff --git a/sys-infiniband/libibcm/libibcm-1.0.4.ebuild b/sys-infiniband/libibcm/libibcm-1.0.4.ebuild
index 5f860da43..050e3b927 100644
--- a/sys-infiniband/libibcm/libibcm-1.0.4.ebuild
+++ b/sys-infiniband/libibcm/libibcm-1.0.4.ebuild
@@ -15,7 +15,7 @@ DESCRIPTION="OpenIB Userspace CM library"
 KEYWORDS="~x86 ~amd64"
 IUSE=""
 
-RDEPEND=">=sys-cluster/libibverbs-1.1.2"
+RDEPEND=">=sys-infiniband/libibverbs-1.1.2"
 DEPEND="${RDEPEND}"
 
 src_install() {
diff --git a/sys-infiniband/libibcommon/Manifest b/sys-infiniband/libibcommon/Manifest
index 67eba0927..0eaf3ef56 100644
--- a/sys-infiniband/libibcommon/Manifest
+++ b/sys-infiniband/libibcommon/Manifest
@@ -1,14 +1,4 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee
-EBUILD libibcommon-1.1.2_p20081020.ebuild 464 RMD160 233cf4ef801b03be0db36fea394d5c3b30413ccb SHA1 db59c383181d925472305772adbbd55c10e993e8 SHA256 f99754ca40b887a4de8a1b0d763997cad4de0504467aa282a6ceeee145d23036
+EBUILD libibcommon-1.1.2_p20081020.ebuild 467 RMD160 ae48164c21c92afa6dac396f94e573e9e3b78fd1 SHA1 afaf52d38ec745acdda56d327db40a23d079867d SHA256 5ae97bf34e09b3b390af57e7a677f03925a8b5c9ee1577e07be53e4b7d7c5b5b
 MISC ChangeLog 1102 RMD160 8b6f9fbe410fd43721bb7e0edc68ad51d3d880fd SHA1 88b0a70e548076d790755a5b83bff5d94ec8141d SHA256 7255900509d988e58efddce3ee2559ea3492a53d4b9f55389bc923a221f62008
 MISC metadata.xml 294 RMD160 77f1de3facb664ac1013b3111ecab082fbe47d9a SHA1 54c68a26e5636f2a476a5b9307466d3736898aa7 SHA256 5bb76f6e785f99b3a0ef6683660008d37d49fd13b64742c7945565d14b3ea23e
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.10 (GNU/Linux)
-
-iEYEARECAAYFAknC040ACgkQ5BmOA85PVLj9PwCeLQVDjm7BtyWy5rPk3dn40e+w
-CgsAn0qqDHsTGfqn9EmyaiOuQZwI3ymV
-=WCLd
------END PGP SIGNATURE-----
diff --git a/sys-infiniband/libibcommon/libibcommon-1.1.2_p20081020.ebuild b/sys-infiniband/libibcommon/libibcommon-1.1.2_p20081020.ebuild
index 5b8ea6615..fed8d5eee 100644
--- a/sys-infiniband/libibcommon/libibcommon-1.1.2_p20081020.ebuild
+++ b/sys-infiniband/libibcommon/libibcommon-1.1.2_p20081020.ebuild
@@ -15,7 +15,7 @@ IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}
-	!sys-cluster/openib-userspace"
+	!sys-infiniband/openib-userspace"
 
 src_install() {
 	make DESTDIR="${D}" install || die "install failed"
diff --git a/sys-infiniband/libibmad/Manifest b/sys-infiniband/libibmad/Manifest
index 9c501d65e..fd0feef3d 100644
--- a/sys-infiniband/libibmad/Manifest
+++ b/sys-infiniband/libibmad/Manifest
@@ -1,14 +1,4 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee
-EBUILD libibmad-1.2.3_p20081118.ebuild 524 RMD160 2a10f9eb04ebe7dc515d1ac1bc45025b0d8308e6 SHA1 492b23a101fc645b5254ccec122e7e5bcadf428f SHA256 939f5d3b36f5913fcee59e77f1347064b5148d83292358abf92a1b0c6f4068b1
+EBUILD libibmad-1.2.3_p20081118.ebuild 530 RMD160 e10e9bc7daf75405d8b79da253bc20a9b31a7159 SHA1 2f237f33ab93b5ae6bc3e5467044ee79c5afc8c9 SHA256 985d26fde8b0333df1b749b123031a160359d5833899ba17f286c4757500a0c1
 MISC ChangeLog 1108 RMD160 249c2ea55ca1da94095c5906d3420985b1d7f546 SHA1 207b35028cf57b409e78ff40ae7f61f9f3f5de50 SHA256 a530cea229c0533ae0da544b38d0c3eb315b45f710b6c0b52c26a5c6e4a7ee47
 MISC metadata.xml 361 RMD160 c9e07faec64931dfdbcae2c0e0736d351da10073 SHA1 bb009860a1a59bd35a7558a41be11d6983f45978 SHA256 4a424c126404f43935a79b2c4097c40a8e5f9d8b8edb39ecd6e4b07c37a61451
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.10 (GNU/Linux)
-
-iEYEARECAAYFAknC05IACgkQ5BmOA85PVLgmkACfVWNODLmuvWNZCL+NYD32FFsz
-kaUAoKZ/aXISclxB3J+LlVRRSWPTrmUI
-=7C8U
------END PGP SIGNATURE-----
diff --git a/sys-infiniband/libibmad/libibmad-1.2.3_p20081118.ebuild b/sys-infiniband/libibmad/libibmad-1.2.3_p20081118.ebuild
index c82d72f47..3f45e5ce0 100644
--- a/sys-infiniband/libibmad/libibmad-1.2.3_p20081118.ebuild
+++ b/sys-infiniband/libibmad/libibmad-1.2.3_p20081118.ebuild
@@ -13,8 +13,8 @@ DESCRIPTION="OpenIB library that provides low layer IB functions for use by the
 KEYWORDS="~x86 ~amd64"
 IUSE=""
 
-DEPEND=">=sys-cluster/libibcommon-1.1.2_p20081020
-		>=sys-cluster/libibumad-1.2.3_p20081118"
+DEPEND=">=sys-infiniband/libibcommon-1.1.2_p20081020
+		>=sys-infiniband/libibumad-1.2.3_p20081118"
 RDEPEND="${DEPEND}"
 
 src_install() {
diff --git a/sys-infiniband/libibumad/Manifest b/sys-infiniband/libibumad/Manifest
index c1cf87232..c3a96120c 100644
--- a/sys-infiniband/libibumad/Manifest
+++ b/sys-infiniband/libibumad/Manifest
@@ -1,14 +1,4 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee
-EBUILD libibumad-1.2.3_p20081118.ebuild 467 RMD160 19745233d55d5c3196ff29d97361a117ae3bfaa8 SHA1 939f2a841ffab31fbcfb376ed13ed42fa6e8940a SHA256 9fc259946f18d8c807a81d6df82d7335024a55bc9bb38281ea818fc7d350e922
+EBUILD libibumad-1.2.3_p20081118.ebuild 470 RMD160 e5def0d4cda71853005bf11545f7598e47e89292 SHA1 42dd9570f79e1dad7210430b9ac5399c98c74a2c SHA256 0892b35e91f97ca4a44faad5e1809517c47d0a4b4a35a782bdc0b30903850aed
 MISC ChangeLog 1122 RMD160 753809a89d8aff8a8d06bf7fbf7d6955b9b5951d SHA1 e4bbcd009cd20e619967be7f6209ae35415f067b SHA256 8cda0c9a748902fa504b4336a4fd795efc3df65b0a3d7311a938b4707d70cb19
 MISC metadata.xml 364 RMD160 b8bcb6c91bc52a35c0ba1d2f63d1eb14120bb216 SHA1 efad3cefe8ed0c8058ecffee15b901d06807e34f SHA256 114ee13c84a4f6aa6cc13f8cd91216d9bac7d504795ee4fd7b8f4598b1f82a5d
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.10 (GNU/Linux)
-
-iEYEARECAAYFAknC05YACgkQ5BmOA85PVLiamQCeMqi0JZhrE2Zqie05d3tL2gJs
-AlAAniJKrfBLXB8F9GzhnQVKzEG2iZxc
-=W1wk
------END PGP SIGNATURE-----
diff --git a/sys-infiniband/libibumad/libibumad-1.2.3_p20081118.ebuild b/sys-infiniband/libibumad/libibumad-1.2.3_p20081118.ebuild
index 62ef149eb..a576e3335 100644
--- a/sys-infiniband/libibumad/libibumad-1.2.3_p20081118.ebuild
+++ b/sys-infiniband/libibumad/libibumad-1.2.3_p20081118.ebuild
@@ -13,7 +13,7 @@ DESCRIPTION="OpenIB User MAD library functions which sit on top of the user MAD
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND=">=sys-cluster/libibcommon-1.1.2_p20081020"
+DEPEND=">=sys-infiniband/libibcommon-1.1.2_p20081020"
 RDEPEND="${DEPEND}"
 
 src_install() {
diff --git a/sys-infiniband/libibverbs/Manifest b/sys-infiniband/libibverbs/Manifest
index 7c4479920..e6551a8e7 100644
--- a/sys-infiniband/libibverbs/Manifest
+++ b/sys-infiniband/libibverbs/Manifest
@@ -1,14 +1,4 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee
-EBUILD libibverbs-1.1.2.ebuild 503 RMD160 6a560ec1a9c3df9cb307043529348090584c99c5 SHA1 282d4f9c40f44de97f911ef117437bedac39dab0 SHA256 5459a15d476e1a71f784601a7e7efc4ee7763d5e9d89396177912dfae2024f47
+EBUILD libibverbs-1.1.2.ebuild 506 RMD160 c0983f4c4365aca753d5a174162a289aaca0a242 SHA1 4c7cc76085bd8dcf247c4133b34eab72da31aad9 SHA256 3cee48c20645cd86b157f50d6e52777af4158ca81a9dbd02860bade8f20b398c
 MISC ChangeLog 1460 RMD160 4cb4ad1308cb03830afb9891885ce7649659d5e6 SHA1 d2741dbc36102a619d5f223ef4b77a23444933fa SHA256 42c5fa0f99373a932384bc723ed2addd107df3d0ef662527f8ea0f8c976d375c
 MISC metadata.xml 426 RMD160 9bf509ead397955652dcc89a9cff5370ccaee9bd SHA1 38090b6e7d9e6677943062b81b8ea6a29b5f698d SHA256 041eeefa57c81b2cef7450e96ead60e4d999570cfe9d62cfc4252ff904e18719
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.10 (GNU/Linux)
-
-iEYEARECAAYFAknC05sACgkQ5BmOA85PVLhsYQCeLxfW1QSQARBUcwbL+OvVEiim
-8B4AmwWQB/mFrd/9TxZJp3b81RxyQpu6
-=TI0O
------END PGP SIGNATURE-----
diff --git a/sys-infiniband/libibverbs/libibverbs-1.1.2.ebuild b/sys-infiniband/libibverbs/libibverbs-1.1.2.ebuild
index 7e7a989bd..818caafb4 100644
--- a/sys-infiniband/libibverbs/libibverbs-1.1.2.ebuild
+++ b/sys-infiniband/libibverbs/libibverbs-1.1.2.ebuild
@@ -15,7 +15,7 @@ IUSE=""
 
 DEPEND="sys-fs/sysfsutils"
 RDEPEND="${DEPEND}
-	!sys-cluster/openib-userspace"
+	!sys-infiniband/openib-userspace"
 
 src_install() {
 	make DESTDIR="${D}" install || die "install failed"
diff --git a/sys-infiniband/libipathverbs/Manifest b/sys-infiniband/libipathverbs/Manifest
index b28e5bf37..02eb3075d 100644
--- a/sys-infiniband/libipathverbs/Manifest
+++ b/sys-infiniband/libipathverbs/Manifest
@@ -1,4 +1,4 @@
 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee
-EBUILD libipathverbs-1.1.ebuild 445 RMD160 722de02e003438e7a6ee2db9c342d448f90d4676 SHA1 8107dec2ff1976f0278fd43345654c81e67cdf09 SHA256 9595eca36daaea9b4e340c5cb8a5c6fb115e9ddb22ea05923b4d6e3304eeea98
+EBUILD libipathverbs-1.1.ebuild 448 RMD160 3a74e91b826b9fae3805132b0277cf6d445def40 SHA1 cbb37e3f946b9173936d57e536dbadb3732a34d6 SHA256 537ed132d9d5bbf4d31391baa7e21b0b340cb738ddaa2e1c4ad77deb0b8a9708
 MISC ChangeLog 504 RMD160 a5281f691754e8351d62e9cd48f2badb3afea346 SHA1 fbbfed3e0a4b3b147dbd5ed107023a0071d227e6 SHA256 1246f6e3c36380882a9899f757a431c44b9ec631286ded38dc14814c1dbf2c86
 MISC metadata.xml 421 RMD160 114e8aecda6d8cc32b5e5d6e20706a752acfb247 SHA1 61db2054e6c0443a599c36d23994c71bf4795c46 SHA256 9082167e78422f279b2fa3a85ffd8a795fee49f0726f5a3f34688056eb9818b7
diff --git a/sys-infiniband/libipathverbs/libipathverbs-1.1.ebuild b/sys-infiniband/libipathverbs/libipathverbs-1.1.ebuild
index fce9217df..5774e3480 100644
--- a/sys-infiniband/libipathverbs/libipathverbs-1.1.ebuild
+++ b/sys-infiniband/libipathverbs/libipathverbs-1.1.ebuild
@@ -13,7 +13,7 @@ DESCRIPTION="OpenIB userspace driver for the PathScale InfiniBand HCAs"
 KEYWORDS="~x86 ~amd64"
 IUSE=""
 
-DEPEND=">=sys-cluster/libibverbs-1.1.2"
+DEPEND=">=sys-infiniband/libibverbs-1.1.2"
 RDEPEND="${DEPEND}"
 
 src_install() {
diff --git a/sys-infiniband/libmlx4/Manifest b/sys-infiniband/libmlx4/Manifest
index 367666e53..f3988bc47 100644
--- a/sys-infiniband/libmlx4/Manifest
+++ b/sys-infiniband/libmlx4/Manifest
@@ -1,4 +1,4 @@
 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee
-EBUILD libmlx4-1.0.ebuild 479 RMD160 0ec45f391ad2df72fbdf063b27f826653b4a33a0 SHA1 27998323c4ed25c565af4e471617adfdf07691f0 SHA256 63c5d14916a215e83f07f6b2c5af1f719a2d4b28c91c17d8132d7752af478369
+EBUILD libmlx4-1.0.ebuild 485 RMD160 3824aff96b198d072385af5f9dadc23e29b1f080 SHA1 9bcf51b47f4da51de478f93b68c41139967655a5 SHA256 5d9370e458b27c7c53eb303cae2eefc8aa934a40a40ef70aca2e7aa9b1b7b424
 MISC ChangeLog 253 RMD160 c2ec79c8b76c95a64aa3ba6656bfc8ba68abf11d SHA1 b64ee5cd7ebc764980ad508136d94455204c542b SHA256 ed37b7bbde27e45c98d7bcd0a96616c217efffb2bfce1e09ac90647bc2bfb8d4
 MISC metadata.xml 426 RMD160 9bf509ead397955652dcc89a9cff5370ccaee9bd SHA1 38090b6e7d9e6677943062b81b8ea6a29b5f698d SHA256 041eeefa57c81b2cef7450e96ead60e4d999570cfe9d62cfc4252ff904e18719
diff --git a/sys-infiniband/libmlx4/libmlx4-1.0.ebuild b/sys-infiniband/libmlx4/libmlx4-1.0.ebuild
index db2395a6c..91852cab5 100644
--- a/sys-infiniband/libmlx4/libmlx4-1.0.ebuild
+++ b/sys-infiniband/libmlx4/libmlx4-1.0.ebuild
@@ -13,9 +13,9 @@ DESCRIPTION="OpenIB userspace driver for Mellanox ConnectX HCA"
 KEYWORDS="~x86 ~amd64"
 IUSE=""
 
-DEPEND=">=sys-cluster/libibverbs-1.1.2"
+DEPEND=">=sys-infiniband/libibverbs-1.1.2"
 RDEPEND="${DEPEND}
-	!sys-cluster/openib-userspace"
+	!sys-infiniband/openib-userspace"
 
 src_install() {
 	make DESTDIR="${D}" install || die "install failed"
diff --git a/sys-infiniband/libmthca/Manifest b/sys-infiniband/libmthca/Manifest
index e81414fca..37c55d44f 100644
--- a/sys-infiniband/libmthca/Manifest
+++ b/sys-infiniband/libmthca/Manifest
@@ -1,4 +1,4 @@
 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee
-EBUILD libmthca-1.0.5.ebuild 482 RMD160 ae04365b020d0711a5e381808a6bbdc5bba0d3e2 SHA1 f718a108bf42212b6003052b69d06b0a606c5beb SHA256 956feb9a321d87226da45a3327677987765a04d7708ea197479371af7cc56f12
+EBUILD libmthca-1.0.5.ebuild 488 RMD160 b030a1333697f0da0794d0a05f9a39b65e880134 SHA1 04afe77e8daf487460c9c7544d2b58ec5b41c32e SHA256 256df69d63f3b56d6ff33fb5be942b924fdec4f5085593551c03773dc76fee5a
 MISC ChangeLog 690 RMD160 cf95f555ada02a3d9df957740ff58af2a5d9a092 SHA1 55a8f81dc20cb22feb29218b92ee11c5898024e3 SHA256 0112775c06913fbb73cccd63deed6fd9061f58adf28807fcc71ed28393747e11
 MISC metadata.xml 426 RMD160 9bf509ead397955652dcc89a9cff5370ccaee9bd SHA1 38090b6e7d9e6677943062b81b8ea6a29b5f698d SHA256 041eeefa57c81b2cef7450e96ead60e4d999570cfe9d62cfc4252ff904e18719
diff --git a/sys-infiniband/libmthca/libmthca-1.0.5.ebuild b/sys-infiniband/libmthca/libmthca-1.0.5.ebuild
index 31d2a4b6e..8d4a52371 100644
--- a/sys-infiniband/libmthca/libmthca-1.0.5.ebuild
+++ b/sys-infiniband/libmthca/libmthca-1.0.5.ebuild
@@ -13,9 +13,9 @@ DESCRIPTION="OpenIB userspace driver for Mellanox InfiniBand HCAs"
 KEYWORDS="~x86 ~amd64"
 IUSE=""
 
-DEPEND=">=sys-cluster/libibverbs-1.1.2"
+DEPEND=">=sys-infiniband/libibverbs-1.1.2"
 RDEPEND="${DEPEND}
-	!sys-cluster/openib-userspace"
+	!sys-infiniband/openib-userspace"
 
 src_install() {
 	make DESTDIR="${D}" install || die "install failed"
diff --git a/sys-infiniband/libnes/Manifest b/sys-infiniband/libnes/Manifest
index 895fff3a5..2acb89071 100644
--- a/sys-infiniband/libnes/Manifest
+++ b/sys-infiniband/libnes/Manifest
@@ -1,4 +1,4 @@
 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee
-EBUILD libnes-0.5.ebuild 462 RMD160 953ab3421597f1ba1487b182365b478ae62294cd SHA1 cdc174fb1adcbd74fb09ebfbb7cef57f08042886 SHA256 b79c1fd6ad5c05b6f34f14fb93d96cdb97c7ac487399305bb592cf968c206c40
+EBUILD libnes-0.5.ebuild 468 RMD160 a3a82b366b27fa21ce52fe9a3fd63db080270688 SHA1 7c65de19d36ecdf35cbb41b9963205bb95793ec5 SHA256 c39d68d10f091eea48864942ad4c7b2e78a54aa44210133c76762c28d1fad127
 MISC ChangeLog 250 RMD160 e549aba8a0a971324efe09dc7ff2da9b80ecc8b7 SHA1 9f42e774049229c9370043a730ee86fd248e0c60 SHA256 ee1c6811ceee82a9db001aba7b553635a74f60b2190b94a1debd4c42a5685bf8
 MISC metadata.xml 426 RMD160 9bf509ead397955652dcc89a9cff5370ccaee9bd SHA1 38090b6e7d9e6677943062b81b8ea6a29b5f698d SHA256 041eeefa57c81b2cef7450e96ead60e4d999570cfe9d62cfc4252ff904e18719
diff --git a/sys-infiniband/libnes/libnes-0.5.ebuild b/sys-infiniband/libnes/libnes-0.5.ebuild
index 6b6c1f316..7cb726bf6 100644
--- a/sys-infiniband/libnes/libnes-0.5.ebuild
+++ b/sys-infiniband/libnes/libnes-0.5.ebuild
@@ -13,9 +13,9 @@ DESCRIPTION="NetEffect RNIC Userspace Library"
 KEYWORDS="~x86 ~amd64"
 IUSE=""
 
-DEPEND=">=sys-cluster/libibverbs-1.1.2"
+DEPEND=">=sys-infiniband/libibverbs-1.1.2"
 RDEPEND="${DEPEND}
-	!sys-cluster/openib-userspace"
+	!sys-infiniband/openib-userspace"
 
 src_install() {
 	make DESTDIR="${D}" install || die "install failed"
diff --git a/sys-infiniband/librdmacm/Manifest b/sys-infiniband/librdmacm/Manifest
index 3a159437d..8469f56db 100644
--- a/sys-infiniband/librdmacm/Manifest
+++ b/sys-infiniband/librdmacm/Manifest
@@ -1,4 +1,4 @@
 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee
-EBUILD librdmacm-1.0.8.ebuild 431 RMD160 689d64d040b38c2bb76d48ce3a1bdee61dfd34d7 SHA1 a69b125a1067ed037272d03addde44c9202bf832 SHA256 12645d437578f2c4c7f409762c5e94433fb804178e98d4666fefa731eded051b
+EBUILD librdmacm-1.0.8.ebuild 434 RMD160 b86b108127855eb0238a6b47ba7e14164f49089e SHA1 af796aa448571a195fec34692d4be5275386ece8 SHA256 7d42d3e33e19bbab2d147d483e81f9ce3a3cd2a988a2f244802c026d1ac23c3f
 MISC ChangeLog 731 RMD160 f7e8898122b3243b49c43444b21dd1334becd4d4 SHA1 f68fea74242d529a4afd124a8093af2b15b73389 SHA256 15e6be3c425906861c0ea604c98903ceff4ea014493cd2b263862697d6c8b2ef
 MISC metadata.xml 231 RMD160 4e683cf1e4e98e12f6827c19be6b1507c66d6bc2 SHA1 4cc03d85daa352f1d0b36d7a031765ee30c9ea2e SHA256 dc582f05fc10f90c08881f52d8434a939bf12da38a73004ba0327e5b1bc0bc9d
diff --git a/sys-infiniband/librdmacm/librdmacm-1.0.8.ebuild b/sys-infiniband/librdmacm/librdmacm-1.0.8.ebuild
index be7d5ef82..266b5ced4 100644
--- a/sys-infiniband/librdmacm/librdmacm-1.0.8.ebuild
+++ b/sys-infiniband/librdmacm/librdmacm-1.0.8.ebuild
@@ -14,7 +14,7 @@ KEYWORDS="~x86 ~amd64"
 IUSE=""
 DEPEND=""
 RDEPEND="${DEPEND}
-	!sys-cluster/openib-userspace"
+	!sys-infiniband/openib-userspace"
 
 src_install() {
 	make DESTDIR="${D}" install || die "install failed"
diff --git a/sys-infiniband/openib-diags/Manifest b/sys-infiniband/openib-diags/Manifest
index 543e86089..6ff2e698c 100644
--- a/sys-infiniband/openib-diags/Manifest
+++ b/sys-infiniband/openib-diags/Manifest
@@ -1,15 +1,5 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 AUX openib-diags-1.4.4_p20081207-remove-osmv.patch 11381 RMD160 e84bae73e8866736c6ae50c354a7fde0ada8c9c0 SHA1 d7016beba804524b00cdceb0d5b5f03703186f7f SHA256 35d9b5fe53c003e51cf4942808f06364647622fee6030f22ece3f2115984621a
 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee
-EBUILD openib-diags-1.4.4_p20081207.ebuild 625 RMD160 21767e15fc67c02b9df8201ee5a5e1a89ea3820b SHA1 6f942c447395bca46b54f2984be956294109669f SHA256 273f722d7c0e561dfd0bacac16c53c10f41a6c65b686c2439cfa8f5a3be6fa21
+EBUILD openib-diags-1.4.4_p20081207.ebuild 637 RMD160 507b1b18bf2fcd6c611c5e7999b08756d65f95e5 SHA1 41c5eb16406c1d412b04e6421c1ce2efaa0dca1b SHA256 e44056acc67c38c2475daed69987ec1e433071528be3cbd3d23a78df6a01a81a
 MISC ChangeLog 940 RMD160 7c61c8302e6e9d6dea118074aec587043fa3baa0 SHA1 fd517a0ad8000e494489405c55cb0512a51a4b6e SHA256 0d3ca21e60496eac7275bd490ebcc1c10a503d84b6e6c4b08c7ad65369e1b9ad
 MISC metadata.xml 269 RMD160 313528b9b250be3cefa43fe1e6ae748c039d23ff SHA1 2b1efb89864ecc3dc8688cfff7c17cfe450a9c8b SHA256 84569c739f3fca7d8afe1d90bc7c700cd5435f3101ae16800e1a8af3a4711eee
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.10 (GNU/Linux)
-
-iEYEARECAAYFAknC0N0ACgkQ5BmOA85PVLjBLACeNOAZxZNRZ81cMyeaoEpysHk5
-LeYAn14HUc+q7M+qfYq8xEnaDe7kEE2e
-=zOhO
------END PGP SIGNATURE-----
diff --git a/sys-infiniband/openib-diags/openib-diags-1.4.4_p20081207.ebuild b/sys-infiniband/openib-diags/openib-diags-1.4.4_p20081207.ebuild
index 75f454774..21eac5567 100644
--- a/sys-infiniband/openib-diags/openib-diags-1.4.4_p20081207.ebuild
+++ b/sys-infiniband/openib-diags/openib-diags-1.4.4_p20081207.ebuild
@@ -13,10 +13,10 @@ DESCRIPTION="OpenIB diagnostic programs and scripts needed to diagnose an IB sub
 KEYWORDS="~x86 ~amd64"
 IUSE=""
 
-DEPEND=">=sys-cluster/libibcommon-1.1.2_p20081020
-		>=sys-cluster/libibumad-1.2.3_p20081118
-		>=sys-cluster/libibmad-1.2.3_p20081118
-		>=sys-cluster/openib-osm-3.2.5_p20081207"
+DEPEND=">=sys-infiniband/libibcommon-1.1.2_p20081020
+		>=sys-infiniband/libibumad-1.2.3_p20081118
+		>=sys-infiniband/libibmad-1.2.3_p20081118
+		>=sys-infiniband/openib-osm-3.2.5_p20081207"
 RDEPEND="${DEPEND}"
 
 PATCHES=( "${FILESDIR}/${P}-remove-osmv.patch" )
diff --git a/sys-infiniband/openib-drivers/Manifest b/sys-infiniband/openib-drivers/Manifest
index 860348564..414bf68b3 100644
--- a/sys-infiniband/openib-drivers/Manifest
+++ b/sys-infiniband/openib-drivers/Manifest
@@ -2,7 +2,7 @@ AUX openib 26021 RMD160 2507367b5b588e1ef95b91ec7a2a362f592c8e15 SHA1 b043dcd891
 AUX openib.modprobe 350 RMD160 a40e8656ee1bdfc26a86b65aa3eaf5553a93b7b8 SHA1 623adbeccde3e88ce2c39d113a409c4d14091f0d SHA256 32054c7ee7caffc21ed320a9be5d0c2cd85e51295c0515521373d658f55ee68e
 DIST OFED-1.2.5.1.tgz 46256516 RMD160 b19f1917b32b7b15db75aace6ed433d57dc98fc5 SHA1 9a1ff30c97c94352f70e52d7cc31328013bea1b7 SHA256 41c6408135d8707d05bef8aa0a4ec548ae64ec010224e3b38746ab6f5c1e9b78
 DIST OFED-1.2.5.5.tgz 46432282 RMD160 f5829858fca521d8675af1245d4764eeb87ff08d SHA1 faa027109b56583207eca9fd736164517acf7120 SHA256 ffb990b22d7b0f25026d9fe785aa97ca5920b5a0e620851deb057b9b83bbf907
-EBUILD openib-drivers-1.2.5.1.ebuild 6403 RMD160 2731a255da2108aa3804b88b9a436ed29d6a4ef2 SHA1 cbf9759aac25d30604304db77699b487998e0459 SHA256 834dbe6aeb399f20cd7f8e3b0a1b59643820c7e1f79e61a76c089db806f72ede
+EBUILD openib-drivers-1.2.5.1.ebuild 6406 RMD160 b8459225d680696839a1150630c0d32b89473412 SHA1 ebecc32afc71bafdd0c7634e06814c7d49b19929 SHA256 82e5cfd66852e2f2a98673b6bf41587d29e616e746e51641b0f968d75af29080
 EBUILD openib-drivers-1.2.5.5.ebuild 3939 RMD160 522f4a4aa54041e0f2bd2d66f90e72ba8c41e1ae SHA1 ae7d218df3c765b08b76876ae7c20b289062318c SHA256 6ff86989c1230c6fc89d5aa649d0e3bce93c9f1fc76e26a1d8048be772ef7bb8
 MISC ChangeLog 895 RMD160 6263ab0ef045e071ca9d22b36c056668b31d5b54 SHA1 a513ed90637419a9a51ffed37d25909430a17646 SHA256 1861f1f31364b459b68a2d62975861c0b87c234fdb8e419ab24d7174fc16c43e
 MISC metadata.xml 220 RMD160 d33d570d49f634b36df8f6c179b8385e25562a56 SHA1 fffa23cb3edea7fe576a0d0e470df5750547f1cb SHA256 50078f776034343d365347ef90d5a0eb49faf851ed7f46e12cf9ce71e4cb5ea7
diff --git a/sys-infiniband/openib-drivers/openib-drivers-1.2.5.1.ebuild b/sys-infiniband/openib-drivers/openib-drivers-1.2.5.1.ebuild
index 4ba2d28d1..88b3f0338 100644
--- a/sys-infiniband/openib-drivers/openib-drivers-1.2.5.1.ebuild
+++ b/sys-infiniband/openib-drivers/openib-drivers-1.2.5.1.ebuild
@@ -20,7 +20,7 @@ IUSE="memtrack hpage-patch srp ipath iser ehca rds madeye vnic cxgb3 debug"
 RDEPEND=""
 DEPEND="${RDEPEND}
 	virtual/linux-sources
-	!sys-cluster/openib-files"
+	!sys-infiniband/openib-files"
 
 pkg_setup() {
 
diff --git a/sys-infiniband/openib-mvapich2/Manifest b/sys-infiniband/openib-mvapich2/Manifest
index f361aafb6..7dc8b0504 100644
--- a/sys-infiniband/openib-mvapich2/Manifest
+++ b/sys-infiniband/openib-mvapich2/Manifest
@@ -3,10 +3,10 @@ DIST mvapich2-0.9.5.tar.gz 13873 RMD160 56e146c80be3cd7b5f1e1469f20e2c17549b15d7
 DIST mvapich2-0.9.6.tar.gz 13873 RMD160 56e146c80be3cd7b5f1e1469f20e2c17549b15d7 SHA1 4026f5d3b32fc279a1480842599f0dd1a04b4621 SHA256 1dcd75956f8d947c5cbdeed39d7d39440d9cb0132aa3607042452514ca922d8f
 DIST mvapich2-1.0.1.tar.gz 14062480 RMD160 da9e4dd07998d82ead0276e8b264a487c4d4fe79 SHA1 3edc9720251f8060e0f9c8cc58800a45a66cc7ae SHA256 a20fb87ed674bec3b2de87c47cc3965c33248e00b37f7eb08ba40d0bab07ca5e
 DIST mvapich2-1.0.tar.gz 14061056 RMD160 ba57d0d51bbdd3956dce446575d2ecbed4fe5b2f SHA1 b2f6ecf3e3b06c63b443bbcc55c2043f6d683f67 SHA256 30c0849dc7e8d4581cfee16a824f5e384e8198b60b7f54f880f4e25da7d1c143
-EBUILD openib-mvapich2-0.9.5.ebuild 3227 RMD160 9d0d68e5fa9ff475294aa991094517478f0090ae SHA1 694729bfd02639f65e376187c6366731334c7142 SHA256 1e655c043996f86232e5ac1dab156d21c3fca4c4be3e202bcbb8f75d7b345b74
-EBUILD openib-mvapich2-0.9.6.ebuild 3222 RMD160 722c4dbea3358ebb2810fd47f68433744bf70d59 SHA1 af556fe75370c979e6600c13d3354ffabf3cf027 SHA256 5dae03b9523bf5b72c859f34d41edd53a090ed09faaa00069dae581349a4b9d7
-EBUILD openib-mvapich2-1.0.1-r1.ebuild 4310 RMD160 8f5cceb30096c60d73ff3c111e67a527bd89ae06 SHA1 45c52cf1265e5ff161854233c15fa2d7f471741f SHA256 9bc600bb4c362f9d150ed0a9573b72cdff29494427b400968074872b61f415be
-EBUILD openib-mvapich2-1.0.1.ebuild 3124 RMD160 b5e931451462a275363ff3fe8764f5684deb0c6e SHA1 31f291fd15dd9651442af630be4a7418936ed9f6 SHA256 5748e92e739081c485b98c41b729234ba3bf1aa010fdf4dad6aae99d7732e7ee
-EBUILD openib-mvapich2-1.0.ebuild 3124 RMD160 b5e931451462a275363ff3fe8764f5684deb0c6e SHA1 31f291fd15dd9651442af630be4a7418936ed9f6 SHA256 5748e92e739081c485b98c41b729234ba3bf1aa010fdf4dad6aae99d7732e7ee
+EBUILD openib-mvapich2-0.9.5.ebuild 3239 RMD160 f7a4069ba76fb382c2ee6e86d5ff2d9f8df16b9c SHA1 fbdba2a2e3263ae2905b9faf4f389bfbdca4870d SHA256 36f2eaab54101f737dc0778e551855502da293e4f567fea8012ca3731b78d232
+EBUILD openib-mvapich2-0.9.6.ebuild 3234 RMD160 bb96cb6dab553cd1cf65b49c0a6c2133365c7253 SHA1 6301eef31380d259a07f8a2347f6f0621b006bfc SHA256 5ae2d8c34fa2cec57ebb6a5e4229ac86f3d109ab7d817bd31f896942e198817f
+EBUILD openib-mvapich2-1.0.1-r1.ebuild 4325 RMD160 dca2084b504abfe91fe1f6ee33653411d802bed5 SHA1 b5399eaa26cf688f25bfce23a736b866f8c7ae50 SHA256 b8c5e258d93710920b275f869d597880a5cd79235090b4ed4a381f507479978c
+EBUILD openib-mvapich2-1.0.1.ebuild 3139 RMD160 94391f18ea842c2284ddc5f3a2fbf726a32552b1 SHA1 912eca3e1bb59995b84a7d988c58d5f8323c7542 SHA256 8db00d2a93794610cbfaabb7338e655b547f2e800a831b64572be357bb2be177
+EBUILD openib-mvapich2-1.0.ebuild 3139 RMD160 94391f18ea842c2284ddc5f3a2fbf726a32552b1 SHA1 912eca3e1bb59995b84a7d988c58d5f8323c7542 SHA256 8db00d2a93794610cbfaabb7338e655b547f2e800a831b64572be357bb2be177
 MISC ChangeLog 828 RMD160 46d1432d2147f213a0d29b9989c6ec530b2511c2 SHA1 5e492d39c845a4387e9a7ac67af0b38c2f902a5a SHA256 bc2f305d1bd2516f7bc9f414a199be0a3f7d5148b2de5ffa334b3427a71c45af
 MISC metadata.xml 262 RMD160 2e8cfe97bd1a25814de0657adb7f9ab7f2861895 SHA1 e8a4f573ce01738445befdd0a3e597a79385c0cb SHA256 c54bb4a2708874d3875753c62b071b05f08f6947f71767ac26a4063ad3e4871a
diff --git a/sys-infiniband/openib-mvapich2/openib-mvapich2-0.9.5.ebuild b/sys-infiniband/openib-mvapich2/openib-mvapich2-0.9.5.ebuild
index 09be925a2..0dd97ab0d 100644
--- a/sys-infiniband/openib-mvapich2/openib-mvapich2-0.9.5.ebuild
+++ b/sys-infiniband/openib-mvapich2/openib-mvapich2-0.9.5.ebuild
@@ -21,10 +21,10 @@ S="${WORKDIR}/mvapich2-$PV"
 IUSE="threads debug medium-cluster large-cluster"
 
 DEPEND="
-	|| ( sys-cluster/libibverbs
-	     sys-cluster/openib-userspace )
-	|| ( sys-cluster/librdmacm
-	     sys-cluster/openib-userspace )"
+	|| ( sys-infiniband/libibverbs
+	     sys-infiniband/openib-userspace )
+	|| ( sys-infiniband/librdmacm
+	     sys-infiniband/openib-userspace )"
 RDEPEND="${DEPEND}"
 
 pkg_setup() {
diff --git a/sys-infiniband/openib-mvapich2/openib-mvapich2-0.9.6.ebuild b/sys-infiniband/openib-mvapich2/openib-mvapich2-0.9.6.ebuild
index eb38433cd..c3f7d2285 100644
--- a/sys-infiniband/openib-mvapich2/openib-mvapich2-0.9.6.ebuild
+++ b/sys-infiniband/openib-mvapich2/openib-mvapich2-0.9.6.ebuild
@@ -21,10 +21,10 @@ S="${WORKDIR}/mvapich2-$PV"
 IUSE="threads debug medium-cluster large-cluster"
 
 DEPEND="
-	|| ( sys-cluster/libibverbs
-	     sys-cluster/openib-userspace )
-	|| ( sys-cluster/librdmacm
-	     sys-cluster/openib-userspace )"
+	|| ( sys-infiniband/libibverbs
+	     sys-infiniband/openib-userspace )
+	|| ( sys-infiniband/librdmacm
+	     sys-infiniband/openib-userspace )"
 RDEPEND="${DEPEND}"
 
 pkg_setup() {
diff --git a/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.1-r1.ebuild b/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.1-r1.ebuild
index 3728ff3f7..39bca6c8b 100644
--- a/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.1-r1.ebuild
+++ b/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.1-r1.ebuild
@@ -19,11 +19,11 @@ S="${WORKDIR}/mvapich2-${PV/_/-}"
 IUSE="debug medium-cluster large-cluster rdma romio threads fortran"
 
 RDEPEND="
-	|| ( ( sys-cluster/libibverbs
-			sys-cluster/libibumad
-			sys-cluster/libibmad
-			rdma? ( sys-cluster/librdmacm ) )
-			sys-cluster/openib-userspace )
+	|| ( ( sys-infiniband/libibverbs
+			sys-infiniband/libibumad
+			sys-infiniband/libibmad
+			rdma? ( sys-infiniband/librdmacm ) )
+			sys-infiniband/openib-userspace )
 	$(mpi_imp_deplist)"
 DEPEND="${RDEPEND}"
 
diff --git a/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.1.ebuild b/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.1.ebuild
index 05d00a8f7..d738fff21 100644
--- a/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.1.ebuild
+++ b/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.1.ebuild
@@ -21,11 +21,11 @@ S="${WORKDIR}/mvapich2-${PV/_/-}"
 IUSE="threads debug medium-cluster large-cluster rdma"
 
 RDEPEND="
-	|| ( ( sys-cluster/libibverbs
-	       sys-cluster/libibumad
-		   sys-cluster/libibmad
-	       rdma? ( sys-cluster/librdmacm ) )
-	     sys-cluster/openib-userspace )"
+	|| ( ( sys-infiniband/libibverbs
+	       sys-infiniband/libibumad
+		   sys-infiniband/libibmad
+	       rdma? ( sys-infiniband/librdmacm ) )
+	     sys-infiniband/openib-userspace )"
 DEPEND="${RDEPEND}"
 
 pkg_setup() {
diff --git a/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.ebuild b/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.ebuild
index 05d00a8f7..d738fff21 100644
--- a/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.ebuild
+++ b/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.ebuild
@@ -21,11 +21,11 @@ S="${WORKDIR}/mvapich2-${PV/_/-}"
 IUSE="threads debug medium-cluster large-cluster rdma"
 
 RDEPEND="
-	|| ( ( sys-cluster/libibverbs
-	       sys-cluster/libibumad
-		   sys-cluster/libibmad
-	       rdma? ( sys-cluster/librdmacm ) )
-	     sys-cluster/openib-userspace )"
+	|| ( ( sys-infiniband/libibverbs
+	       sys-infiniband/libibumad
+		   sys-infiniband/libibmad
+	       rdma? ( sys-infiniband/librdmacm ) )
+	     sys-infiniband/openib-userspace )"
 DEPEND="${RDEPEND}"
 
 pkg_setup() {
diff --git a/sys-infiniband/openib-osm/Manifest b/sys-infiniband/openib-osm/Manifest
index 4c9ae8c54..b7672f86d 100644
--- a/sys-infiniband/openib-osm/Manifest
+++ b/sys-infiniband/openib-osm/Manifest
@@ -1,15 +1,5 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 AUX opensm.init.d 711 RMD160 2d2679a8bd09eabdcd4207e77f4dc8cebaa33c1c SHA1 91cefc35cadb03e68ef7c740eac5f417b20cf818 SHA256 e7a32165d81c6065fe0caf1c2fe2709610ac8a24e8e5a0ed342a066a6feb8f94
 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee
-EBUILD openib-osm-3.2.5_p20081207.ebuild 1158 RMD160 3b9b59123c33a52ccd22b769200bd9efc5fbafbe SHA1 dfbd875663ab32d25e4f0696a8328365cdd9c159 SHA256 e63bd58d66deb44780500faeac420419f709b47ea4501e6bd4fa0d45ab5b83f0
+EBUILD openib-osm-3.2.5_p20081207.ebuild 1167 RMD160 46247f24be8d10db11d20d3a1357d50d4c374e51 SHA1 3d01788973abe09dea75ecbc0269be307afe3635 SHA256 53a75d47712db1b51719e3617a52fb5d43ca8f28b4132df01964cf9117ee1079
 MISC ChangeLog 856 RMD160 af629ae1e4644593a473503783116d5557a323a4 SHA1 2d80c50ba6fbfb01f7155989c1508ec6a19cc4ad SHA256 14c2e1d91562d841f9b3c54fb15149868242040093de267f8e27d8287954c5c7
 MISC metadata.xml 419 RMD160 f9b6f7b72f595559b5fdbf3c2bf6cad3490b5900 SHA1 be8a65515c13b833f49766db58e9486961c65078 SHA256 e33518d9908c9e6ee2629959038228160a7215b5b7e04cab593a9734c40df34b
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.10 (GNU/Linux)
-
-iEYEARECAAYFAknCyf4ACgkQ5BmOA85PVLjpYgCfWrWB4kDMAIZG66swdWCD5VD2
-uPUAn2tAqPln3KdQZZTS8pAOHqI1kpsH
-=CQUY
------END PGP SIGNATURE-----
diff --git a/sys-infiniband/openib-osm/openib-osm-3.2.5_p20081207.ebuild b/sys-infiniband/openib-osm/openib-osm-3.2.5_p20081207.ebuild
index 091119bb1..788f75017 100644
--- a/sys-infiniband/openib-osm/openib-osm-3.2.5_p20081207.ebuild
+++ b/sys-infiniband/openib-osm/openib-osm-3.2.5_p20081207.ebuild
@@ -13,10 +13,10 @@ DESCRIPTION="OpenSM - InfiniBand Subnet Manager and Administration for OpenIB"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND=">=sys-cluster/libibmad-1.2.3_p20081118
-		>=sys-cluster/libibumad-1.2.3_p20081118"
+DEPEND=">=sys-infiniband/libibmad-1.2.3_p20081118
+		>=sys-infiniband/libibumad-1.2.3_p20081118"
 RDEPEND="$DEPEND
-		 sys-cluster/openib-files
+		 sys-infiniband/openib-files
 		 net-misc/iputils"
 
 src_configure() {
diff --git a/sys-infiniband/openib-perf/Manifest b/sys-infiniband/openib-perf/Manifest
index d3fe861d4..fe723d3e2 100644
--- a/sys-infiniband/openib-perf/Manifest
+++ b/sys-infiniband/openib-perf/Manifest
@@ -1,4 +1,4 @@
 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee
-EBUILD openib-perf-1.2.ebuild 444 RMD160 2e13cd78938c0ae66c42d9578f21f7b9875eb8f7 SHA1 bd3a668a8e290712d6a13cddebca3a0e126ab421 SHA256 858d958630d64617fc26e301eb481fa0d51c28f4898f3a2455f14ade9bb58346
+EBUILD openib-perf-1.2.ebuild 450 RMD160 da8b2de1cee5903a6433e24d4677925382102f76 SHA1 8c3702d164a6fd703aa61cb77cbfdd17b7c67337 SHA256 54f24cba1a1fe1f8fac4e9abe350533cc061405cd841bc5d780762beed1a2838
 MISC ChangeLog 388 RMD160 2326a7c7c41bfee76bc48ec1c6d21a9f63be0be5 SHA1 7cd2c531e3c3f5ed037a21c4ddc80787dea6d6cd SHA256 349876c40e3be8ff57d617e6835508c13f4f2024fb757e4effdb913d593dfc01
 MISC metadata.xml 229 RMD160 e1401ca7c2210ebd7f7951139300cb05b871720c SHA1 847c1c0aca9c9a309fc80aa1345fa6b9df91c5c1 SHA256 30506429bac849161d32a0e3960a93cfacd4e931f8b6cb986965e3a4239ac8c0
diff --git a/sys-infiniband/openib-perf/openib-perf-1.2.ebuild b/sys-infiniband/openib-perf/openib-perf-1.2.ebuild
index bc5d846b6..1ca0caf9c 100644
--- a/sys-infiniband/openib-perf/openib-perf-1.2.ebuild
+++ b/sys-infiniband/openib-perf/openib-perf-1.2.ebuild
@@ -13,8 +13,8 @@ DESCRIPTION="OpenIB uverbs micro-benchmarks"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND=">=sys-cluster/libibverbs-1.1.2
-		>=sys-cluster/librdmacm-1.0.8"
+DEPEND=">=sys-infiniband/libibverbs-1.1.2
+		>=sys-infiniband/librdmacm-1.0.8"
 
 src_compile() {
 	emake || die "emake failed"
diff --git a/sys-infiniband/openib-userspace/Manifest b/sys-infiniband/openib-userspace/Manifest
index f6d202adc..09abbc4ce 100644
--- a/sys-infiniband/openib-userspace/Manifest
+++ b/sys-infiniband/openib-userspace/Manifest
@@ -3,8 +3,8 @@ AUX opensm.init.d 835 RMD160 645d929c491f26d5615c536e40cf5b54b8b7369a SHA1 d7520
 DIST OFED-1.2.5.1.tgz 46256516 RMD160 b19f1917b32b7b15db75aace6ed433d57dc98fc5 SHA1 9a1ff30c97c94352f70e52d7cc31328013bea1b7 SHA256 41c6408135d8707d05bef8aa0a4ec548ae64ec010224e3b38746ab6f5c1e9b78
 DIST OFED-1.2.5.5.tgz 46432282 RMD160 f5829858fca521d8675af1245d4764eeb87ff08d SHA1 faa027109b56583207eca9fd736164517acf7120 SHA256 ffb990b22d7b0f25026d9fe785aa97ca5920b5a0e620851deb057b9b83bbf907
 DIST OFED-1.2.tgz 45785235 RMD160 22abc8ea493c01f18a5ca93f24645c0b3de81f49 SHA1 e179640b8f700b6dff9cc747910d786bba986175 SHA256 05ac6c3a96902388b40b05c6af0f0ce80059fc51980a039d53bfc94874166144
-EBUILD openib-userspace-1.2.5.1-r1.ebuild 2970 RMD160 9f8dea8dcdce524c9892fbafe4570d713fb1cb2d SHA1 bcb9c05bb4d4de44084cf4062ac0480a49e42239 SHA256 cd924caeab3becc0fe13e41cda98c31d84e4a31289e429aaa4b65ea5cd80e1a8
-EBUILD openib-userspace-1.2.5.5.ebuild 2775 RMD160 2c13327d4997d3a4ff56c1fcbf9eb03f23f14458 SHA1 f911a9df2a16e8aed7eda26336db1fa2f4139867 SHA256 407298f19826c1795d40ee2d94413f3cb2efaa3ee363ad6b5c6accb51551de0d
-EBUILD openib-userspace-1.2.ebuild 2615 RMD160 09d862b0bdd376715b0ec41ae4d0fd9a48ddba49 SHA1 92e539361230963c1cb175aea8e60cd980674987 SHA256 33b5df60d3e8049639e47ec16b39e07ad8fd8bb028f52f7df448c761db936be1
+EBUILD openib-userspace-1.2.5.1-r1.ebuild 3027 RMD160 64ea2851a66eeabaacf5d6425d0c09d6f60b3c5c SHA1 2135c63c540d38afd271c00ce003692a9e329354 SHA256 71fe087dbfa3495aa3ecc911c33634f1aa01e8c0d6de1ef3545bad917401f51b
+EBUILD openib-userspace-1.2.5.5.ebuild 2826 RMD160 08f330716c0789aaff76069b49b3996f065f3679 SHA1 633bcc0cf3ce199fa958e82ca823ac41efa3d14b SHA256 926f1084f242f483e50b2bf1cdf7f541c63ddc7dfe835a8682c1d5e371b23589
+EBUILD openib-userspace-1.2.ebuild 2675 RMD160 6f0b0cf57ac739e8cedebbb8b86355c79328cca8 SHA1 40e5a13c968de73d83bf669cd3784d02c5974d34 SHA256 f39b51fc4d9e49c127fccc10accbed0accc5dcf6bdc49bdd046b7f68935762cc
 MISC ChangeLog 930 RMD160 7f896de7f67d0e05d717429577f217a39f4ca8b6 SHA1 bc46a4100c7b63d0b29c12338dc32d63f7ead9ee SHA256 2e3f89049910bc854b1174a4c38b59e78d9bab9f07e38ac2d615e3a8f4570c94
 MISC metadata.xml 290 RMD160 8deacc2efb676788b32b4961d7f30b1b968e057c SHA1 3a6a067aef6960a9d8ddc5f26d12a5d7653cb19d SHA256 86cfc299f76b8bdda514e8817c8ef3a4d49de1938ccc79bdcb98a73dcbc4d6a3
diff --git a/sys-infiniband/openib-userspace/openib-userspace-1.2.5.1-r1.ebuild b/sys-infiniband/openib-userspace/openib-userspace-1.2.5.1-r1.ebuild
index bbf38b9ec..31221cd5d 100644
--- a/sys-infiniband/openib-userspace/openib-userspace-1.2.5.1-r1.ebuild
+++ b/sys-infiniband/openib-userspace/openib-userspace-1.2.5.1-r1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2008 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /CVS/groups/vistech/bgreen-overlay/sys-cluster/openib-userspace/openib-userspace-1.2.ebuild,v 1.1.1.1 2007/10/12 20:18:26 bgreen Exp $
+# $Header: /CVS/groups/vistech/bgreen-overlay/sys-infiniband/openib-userspace/openib-userspace-1.2.ebuild,v 1.1.1.1 2007/10/12 20:18:26 bgreen Exp $
 
 inherit rpm
 
@@ -23,24 +23,24 @@ IUSE="ehca ipath cxgb3 opensm dapl srptools qlvnictools tvflash mstflint"
 
 DEPEND=""
 RDEPEND="${DEPEND}
-		 !<=sys-cluster/openib-drivers-1.2
-		 !sys-cluster/libibverbs
-		 !sys-cluster/libmthca
-		 !sys-cluster/libipathverbs
-		 !sys-cluster/librdmacm
-		 !sys-cluster/libsdp
-		 !sys-cluster/dapl
-		 !sys-cluster/libehca
-		 !sys-cluster/libibcm
-		 !sys-cluster/libibcommon
-		 !sys-cluster/libibmad
-		 !sys-cluster/libibumad
-		 !sys-cluster/openib-diags
-		 !sys-cluster/openib-files
-		 !sys-cluster/openib-osm
-		 !sys-cluster/openib-perf
-		 !sys-cluster/openib-srptools
-		 !sys-cluster/openib"
+		 !<=sys-infiniband/openib-drivers-1.2
+		 !sys-infiniband/libibverbs
+		 !sys-infiniband/libmthca
+		 !sys-infiniband/libipathverbs
+		 !sys-infiniband/librdmacm
+		 !sys-infiniband/libsdp
+		 !sys-infiniband/dapl
+		 !sys-infiniband/libehca
+		 !sys-infiniband/libibcm
+		 !sys-infiniband/libibcommon
+		 !sys-infiniband/libibmad
+		 !sys-infiniband/libibumad
+		 !sys-infiniband/openib-diags
+		 !sys-infiniband/openib-files
+		 !sys-infiniband/openib-osm
+		 !sys-infiniband/openib-perf
+		 !sys-infiniband/openib-srptools
+		 !sys-infiniband/openib"
 
 src_unpack() {
 	unpack ${A} || die "unpack failed"
diff --git a/sys-infiniband/openib-userspace/openib-userspace-1.2.5.5.ebuild b/sys-infiniband/openib-userspace/openib-userspace-1.2.5.5.ebuild
index 4b1ed98b7..d8bbe3b30 100644
--- a/sys-infiniband/openib-userspace/openib-userspace-1.2.5.5.ebuild
+++ b/sys-infiniband/openib-userspace/openib-userspace-1.2.5.5.ebuild
@@ -22,24 +22,24 @@ OSM="${S}/src/userspace/management/osm"
 IUSE="ehca ipath cxgb3 opensm dapl srptools qlvnictools tvflash mstflint"
 
 DEPEND=""
-PDEPEND="=sys-cluster/openib-files-${PV}"
+PDEPEND="=sys-infiniband/openib-files-${PV}"
 RDEPEND="${DEPEND}
-		 !sys-cluster/libibverbs
-		 !sys-cluster/libmthca
-		 !sys-cluster/libipathverbs
-		 !sys-cluster/librdmacm
-		 !sys-cluster/libsdp
-		 !sys-cluster/dapl
-		 !sys-cluster/libehca
-		 !sys-cluster/libibcm
-		 !sys-cluster/libibcommon
-		 !sys-cluster/libibmad
-		 !sys-cluster/libibumad
-		 !sys-cluster/openib-diags
-		 !sys-cluster/openib-osm
-		 !sys-cluster/openib-perf
-		 !sys-cluster/openib-srptools
-		 !sys-cluster/openib"
+		 !sys-infiniband/libibverbs
+		 !sys-infiniband/libmthca
+		 !sys-infiniband/libipathverbs
+		 !sys-infiniband/librdmacm
+		 !sys-infiniband/libsdp
+		 !sys-infiniband/dapl
+		 !sys-infiniband/libehca
+		 !sys-infiniband/libibcm
+		 !sys-infiniband/libibcommon
+		 !sys-infiniband/libibmad
+		 !sys-infiniband/libibumad
+		 !sys-infiniband/openib-diags
+		 !sys-infiniband/openib-osm
+		 !sys-infiniband/openib-perf
+		 !sys-infiniband/openib-srptools
+		 !sys-infiniband/openib"
 
 src_unpack() {
 	unpack ${A} || die "unpack failed"
diff --git a/sys-infiniband/openib-userspace/openib-userspace-1.2.ebuild b/sys-infiniband/openib-userspace/openib-userspace-1.2.ebuild
index 3a8359da5..02d1ee458 100644
--- a/sys-infiniband/openib-userspace/openib-userspace-1.2.ebuild
+++ b/sys-infiniband/openib-userspace/openib-userspace-1.2.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2008 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /CVS/groups/vistech/bgreen-overlay/sys-cluster/openib-userspace/openib-userspace-1.2.ebuild,v 1.1.1.1 2007/10/12 20:18:26 bgreen Exp $
+# $Header: /CVS/groups/vistech/bgreen-overlay/sys-infiniband/openib-userspace/openib-userspace-1.2.ebuild,v 1.1.1.1 2007/10/12 20:18:26 bgreen Exp $
 
 inherit rpm
 
@@ -21,25 +21,25 @@ IUSE="ehca ipath cxgb3 opensm dapl srptools qlvnictools tvflash mstflint"
 
 DEPEND=""
 RDEPEND="${DEPEND}
-		 >=sys-cluster/openib-drivers-1.2
-		 !sys-cluster/libibverbs
-		 !sys-cluster/libmthca
-		 !sys-cluster/libipathverbs
-		 !sys-cluster/librdmacm
-		 !sys-cluster/libsdp
-		 !sys-cluster/dapl
-		 !sys-cluster/libehca
-		 !sys-cluster/libibcm
-		 !sys-cluster/libibcommon
-		 !sys-cluster/libibmad
-		 !sys-cluster/libibumad
-		 !sys-cluster/openib-diags
-		 !sys-cluster/openib-files
-		 !sys-cluster/openib-mvapich2
-		 !sys-cluster/openib-osm
-		 !sys-cluster/openib-perf
-		 !sys-cluster/openib-srptools
-		 !sys-cluster/openib"
+		 >=sys-infiniband/openib-drivers-1.2
+		 !sys-infiniband/libibverbs
+		 !sys-infiniband/libmthca
+		 !sys-infiniband/libipathverbs
+		 !sys-infiniband/librdmacm
+		 !sys-infiniband/libsdp
+		 !sys-infiniband/dapl
+		 !sys-infiniband/libehca
+		 !sys-infiniband/libibcm
+		 !sys-infiniband/libibcommon
+		 !sys-infiniband/libibmad
+		 !sys-infiniband/libibumad
+		 !sys-infiniband/openib-diags
+		 !sys-infiniband/openib-files
+		 !sys-infiniband/openib-mvapich2
+		 !sys-infiniband/openib-osm
+		 !sys-infiniband/openib-perf
+		 !sys-infiniband/openib-srptools
+		 !sys-infiniband/openib"
 
 src_unpack() {
 	unpack ${A} || die "unpack failed"
diff --git a/sys-infiniband/openib/Manifest b/sys-infiniband/openib/Manifest
index ea9cacc4e..978562d59 100644
--- a/sys-infiniband/openib/Manifest
+++ b/sys-infiniband/openib/Manifest
@@ -1,13 +1,3 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
-EBUILD openib-1.4.ebuild 946 RMD160 f69fd0d60ce9161f0d3042d36062f4603c027905 SHA1 2b55fa428a6dbcde396b988afeb3a218e26506d7 SHA256 fde98d15510ad35d61e96cd16bd015d40325d40a2be776ea2da7e5b3bdd89fbc
+EBUILD openib-1.4.ebuild 991 RMD160 23d9c3ffc78bbf16eea53f1503ebfc77878a3091 SHA1 ca3cc19cfe9fdb7bccaa7c1d6db631e866614786 SHA256 89a366b8f83736a8e1be6309fae9e53df229ca4823d4e8ebcd28e75cf2348c72
 MISC ChangeLog 590 RMD160 7a3088e805845acc5471c28b91c18a2a4496d518 SHA1 daf98c93b161e1cd998223400be2dbc3f8610e25 SHA256 de143abbf7e03cf01712f3c5efa21fd29b3abaa06b4e7483266f6b941153df7a
 MISC metadata.xml 273 RMD160 19db7de67d8f6f506a22dd8adc8cd2e2a562b6bb SHA1 e9d1b4bb8fb0323553f656b2d11cc1cf2a900196 SHA256 8c90385fd9c444052c28524c0d9a29397513de5e72444efabcdf196e76f1e50d
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.10 (GNU/Linux)
-
-iEYEARECAAYFAknC1C8ACgkQ5BmOA85PVLhhgwCgrQHV0YM19CfieVFTA5dws4/D
-6B0AnAzEJ7DAbhPwHLGMDYQNfRmZn/MS
-=iymp
------END PGP SIGNATURE-----
diff --git a/sys-infiniband/openib/openib-1.4.ebuild b/sys-infiniband/openib/openib-1.4.ebuild
index 5fd9bbdbc..4356196d0 100644
--- a/sys-infiniband/openib/openib-1.4.ebuild
+++ b/sys-infiniband/openib/openib-1.4.ebuild
@@ -12,20 +12,20 @@ LICENSE="|| ( GPL-2 BSD-2 )"
 KEYWORDS="~amd64 ~x86"
 IUSE="+dapl diags ehca ipath mlx4 mthca nes +opensm"
 
-DEPEND=">=sys-cluster/libibcm-1.0.4
-	>=sys-cluster/libibcommon-1.1.2_p20081020
-	>=sys-cluster/libibmad-1.2.3_p20081118
-	>=sys-cluster/libibumad-1.2.3_p20081118
-	>=sys-cluster/openib-files-${PV}
-	>=sys-cluster/libsdp-1.1.99
-	>=sys-cluster/openib-perf-1.2
-	dapl? ( >=sys-cluster/dapl-2.0.15 )
-	diags? ( >=sys-cluster/openib-diags-1.4.4_p20081207 )
-	ehca? ( >=sys-cluster/libehca-1.2.1 )
-	ipath? ( >=sys-cluster/libipathverbs-1.1 )
-	mlx4? ( >=sys-cluster/libmlx4-1.0 )
-	mthca? ( >=sys-cluster/libmthca-1.0.5 )
-	nes? ( >=sys-cluster/libnes-0.5 )
-	opensm? ( >=sys-cluster/openib-osm-3.2.5_p20081207 )"
+DEPEND=">=sys-infiniband/libibcm-1.0.4
+	>=sys-infiniband/libibcommon-1.1.2_p20081020
+	>=sys-infiniband/libibmad-1.2.3_p20081118
+	>=sys-infiniband/libibumad-1.2.3_p20081118
+	>=sys-infiniband/openib-files-${PV}
+	>=sys-infiniband/libsdp-1.1.99
+	>=sys-infiniband/openib-perf-1.2
+	dapl? ( >=sys-infiniband/dapl-2.0.15 )
+	diags? ( >=sys-infiniband/openib-diags-1.4.4_p20081207 )
+	ehca? ( >=sys-infiniband/libehca-1.2.1 )
+	ipath? ( >=sys-infiniband/libipathverbs-1.1 )
+	mlx4? ( >=sys-infiniband/libmlx4-1.0 )
+	mthca? ( >=sys-infiniband/libmthca-1.0.5 )
+	nes? ( >=sys-infiniband/libnes-0.5 )
+	opensm? ( >=sys-infiniband/openib-osm-3.2.5_p20081207 )"
 RDEPEND="${DEPEND}"