Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

# By Justin Lecher (20) and others
# Via Jens-Malte Gottfried (1) and Justin Lecher (1)
* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci: (41 commits)
  fix to build petsc in Gentoo Prefix (thanks to Matthias Maier)
  live ebuild update
  live ebuild update
  updated package.mask
  cmake-utils.eclass got merged in gx86
  hybrid stuff got merged
  [sci-mathematics/scilab] fix errors in previous commit
  [sci-mathematics/scilab] version bump
  [dev-java/scirenderer] version bump
  version bump
  app-benchmarks/numbench: Updated dependency for eselect alternatives
  sci-libs/mkl: Version bump
  sci-libs/acml: Version bump
  [sci-mathematics/scilab] update dependencies
  [dev-java/scirenderer] version bump
  [dev-java/jlatexmath-fop] version bump
  [dev-java/jlatexmath] version bump
  app-admin/eselect: rev-bumped to avoid conflict with tree
  sci-chemistry/specView: Needs webkit support in pyside
  sci-chemistry/chemBuild: Needs webkit support in pyside
  ...

Conflicts:
	app-admin/eselect/ChangeLog
	app-admin/eselect/Manifest

22 files changed, 461 insertions, 21 deletions

diff --git a/sci-chemistry/chemBuild/ChangeLog b/sci-chemistry/chemBuild/ChangeLog
new file mode 100644
index 000000000..a592f6b45
--- /dev/null
+++ b/sci-chemistry/chemBuild/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for sci-chemistry/chemBuild
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  21 Sep 2012; Justin Lecher <jlec@gentoo.org> chemBuild-1.0.2.ebuild:
+  Needs webkit support in pyside
+
+*chemBuild-1.0.2 (21 Sep 2012)
+
+  21 Sep 2012; Justin Lecher <jlec@gentoo.org> +chemBuild-1.0.2.ebuild,
+  +files/chemBuild, +metadata.xml:
+  New addition
+
diff --git a/sci-chemistry/chemBuild/Manifest b/sci-chemistry/chemBuild/Manifest
new file mode 100644
index 000000000..2ba5517a2
--- /dev/null
+++ b/sci-chemistry/chemBuild/Manifest
@@ -0,0 +1 @@
+DIST chemBuild1.0.2_WithApi.tar.gz 15593107 SHA256 f27c5f7c5e557af2cbe1ccdacff6e0896ab041536d127733478d27a963bf2f2c SHA512 85cc5d83c63b230c889bbdeed560ac7043db477d7f1a54e42cc85d6b18733b0279e6de0d3e3f1e3b30eb99f450a236a673eb3202d4e0942a20e857ec285df037 WHIRLPOOL ab8f51284056921cb4eb1cf812cd715036ba38547bb1931e187430b5dd2b01315bfebe12a6ef8de9d57fc6c54acb095dbdef53d60eae86d2f116861ed4f5600c
diff --git a/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild b/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild
new file mode 100644
index 000000000..dece95eb2
--- /dev/null
+++ b/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+PYTHON_DEPEND="2"
+
+inherit python toolchain-funcs
+
+DESCRIPTION="Graphical tool to construct chemical compound definitions for NMR"
+HOMEPAGE="http://www.ccpn.ac.uk/software/chembuild"
+SRC_URI="http://www2.ccpn.ac.uk/download/ccpnmr/${PN}${PV}_WithApi.tar.gz"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="dev-python/pyside[webkit]"
+DEPEND=""
+
+S="${WORKDIR}"/ccpnmr/ccpnmr3.0/
+
+#TODO:
+#install in sane place
+#unbundle data model
+#unbundle inchi
+#parallel build
+
+pkg_setup() {
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_install() {
+	local in_path=$(python_get_sitedir)/${PN}
+	local _file
+
+	find . -name "*.pyc" -type f -delete
+	dodir /usr/bin
+	sed \
+	-e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
+	-e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
+	-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
+	-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
+	-e "s|gentoopython|$(PYTHON -a)|g" \
+	-e "s|gentoousr|${EPREFIX}/usr|g" \
+	-e "s|//|/|g" \
+		"${FILESDIR}"/${PN} > "${ED}"/usr/bin/${PN} || die
+	fperms 755 /usr/bin/${PN}
+
+	insinto ${in_path}
+
+	rm -rf cNg license || die
+
+	ebegin "Installing main files"
+		doins -r *
+	eend
+}
+
+pkg_postinst() {
+	python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup ${PN}
+}
diff --git a/sci-chemistry/chemBuild/files/chemBuild b/sci-chemistry/chemBuild/files/chemBuild
new file mode 100644
index 000000000..c6d3d31ac
--- /dev/null
+++ b/sci-chemistry/chemBuild/files/chemBuild
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+export CCPNMR_TOP_DIR=gentoo_sitedir
+export PYTHONPATH=.:${CCPNMR_TOP_DIR}/chemBuild/python
+export LD_LIBRARY_PATH=gentoolibdir
+export TCL_LIBRARY=gentootcl
+export TK_LIBRARY=gentootk
+export PSIPRED_DIR=gentoousr
+gentoopython -O ${CCPNMR_TOP_DIR}/chemBuild/python/ccpnmr/chemBuild/ChemBuild.py $@
diff --git a/sci-chemistry/chemBuild/metadata.xml b/sci-chemistry/chemBuild/metadata.xml
new file mode 100644
index 000000000..d369d068f
--- /dev/null
+++ b/sci-chemistry/chemBuild/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</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/chimera-bin/ChangeLog b/sci-chemistry/chimera-bin/ChangeLog
new file mode 100644
index 000000000..3b78d92d6
--- /dev/null
+++ b/sci-chemistry/chimera-bin/ChangeLog
@@ -0,0 +1,16 @@
+# ChangeLog for sci-chemistry/chimera-bin
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  21 Sep 2012; Justin Lecher <jlec@gentoo.org> chimera-bin-1.6.2.ebuild:
+  Don't strip
+
+  21 Sep 2012; Justin Lecher <jlec@gentoo.org> chimera-bin-1.6.2.ebuild:
+  Set rpath on prefix
+
+*chimera-bin-1.6.2 (20 Sep 2012)
+
+  20 Sep 2012; Justin Lecher <jlec@gentoo.org> +chimera-bin-1.6.2.ebuild,
+  +metadata.xml:
+  New addition
+
diff --git a/sci-chemistry/chimera-bin/Manifest b/sci-chemistry/chimera-bin/Manifest
new file mode 100644
index 000000000..7d8ba0309
--- /dev/null
+++ b/sci-chemistry/chimera-bin/Manifest
@@ -0,0 +1,2 @@
+DIST chimera-1.6.2-linux.bin 83913372 SHA256 06285c0beb3dd61af98fcc5f7d3e0d71e90dd2c26070d9db8ee0c71dae378487 SHA512 3de715261eaafe3c4435221e919196e38ebc5a5815a2df6b035c45797be3a164a55d535b0cb774e588b9ffaee00c70bbb907d558be910fc13c5a8ccdf1fee5e3 WHIRLPOOL 47aa46b0d67a73a19a13619cccbbe7f4c41aba83f3616647d5390d14639a4335dcab7f209129a18f75400240114f1b40cf525e30c9269f6af88ebb9f5025c6f0
+DIST chimera-1.6.2-linux_x86_64.bin 89089984 SHA256 b5ade75e5759e53d29153b4dc3a88fd2fab501e4aa1599efd0f46a1b46e7bd2c SHA512 9cdb99167e39084c483ba192d921c45fbe54b453f71fa24d39eac307f24f799dcd3cc6b0374904f4e9c4836161d81864c5204dda07383a422732b5f81936b59b WHIRLPOOL 0cb90af5b073443aa6b432842fef4371941e684b9fcde6adf0e80a4abcc9654e1e80cd817acb0b9741dc43b9ac33b67b648c0f29d9b938fdb86de0550bd07140
diff --git a/sci-chemistry/chimera-bin/chimera-bin-1.6.2.ebuild b/sci-chemistry/chimera-bin/chimera-bin-1.6.2.ebuild
new file mode 100644
index 000000000..50ba959df
--- /dev/null
+++ b/sci-chemistry/chimera-bin/chimera-bin-1.6.2.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+inherit eutils
+
+DESCRIPTION="An extensible Molecular Modelling System"
+HOMEPAGE="http://www.cgl.ucsf.edu/chimera"
+SRC_URI="
+	amd64? ( chimera-1.6.2-linux_x86_64.bin )
+	x86? ( chimera-1.6.2-linux.bin )"
+
+SLOT="0"
+LICENSE="chimera"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND="prefix? ( dev-util/patchelf )"
+
+S="${WORKDIR}"
+
+RESTRICT="fetch strip"
+
+QA_PREBUILT="opt/.*"
+
+pkg_nofetch() {
+	elog "Please visit"
+	elog "http://www.cgl.ucsf.edu/chimera/download.html"
+	elog "and download ${A} into ${DISTDIR}"
+}
+
+src_unpack() {
+	cp "${DISTDIR}"/${A} ${A}.zip
+	unzip ${A}.zip || die
+}
+
+src_install() {
+	chmod +x ./chimera.bin
+	dodir /opt/
+	./chimera.bin -d foo || die
+	doicon foo/chimeraIcon.png
+	mv foo "${ED}/opt/${PN}" || die
+
+	cat >> "${T}"/chimera <<- EOF
+	#!${EPREFX}/bin/bash
+
+	export PATH="${EPREFIX}/opt/${PN}/bin:\${PATH}"
+	"${EPREFIX}/opt/${PN}/bin/chimera" \$@
+	EOF
+
+	exeinto /opt/bin/
+	doexe "${T}"/chimera
+
+	make_desktop_entry "${EPREFIX}/opt/bin/chimera" Chimera chimeraIcon
+
+	if use prefix; then
+		local i
+		for i in "${ED}"/opt/${PN}/bin/{tiffcp,povray,al2co} "${ED}"/opt/${PN}/lib/*.so; do
+			patchelf --set-rpath "${EPREFIX}/usr/lib:${EPREFIX}/opt/${PN}/lib" "${i}" || die
+		done
+	fi
+}
diff --git a/sci-chemistry/chimera-bin/metadata.xml b/sci-chemistry/chimera-bin/metadata.xml
new file mode 100644
index 000000000..d369d068f
--- /dev/null
+++ b/sci-chemistry/chimera-bin/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</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index e597ab8bd..197705fa3 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  04 Oct 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-9999.ebuild:
+  live ebuild update
+
+  03 Oct 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  metadata.xml:
+  hybrid stuff got merged
+
   09 Aug 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   use ninja if available
 
diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index f54af37be..d95a7cfb9 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -5,7 +5,6 @@
 EAPI="4"
 
 TEST_PV="4.0.4"
-MANUAL_PV="4.5.4"
 
 #to find external blas/lapack
 CMAKE_MIN_VERSION="2.8.5-r2"
@@ -14,8 +13,7 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
 
 inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
 
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
+SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
 
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -23,8 +21,8 @@ if [[ $PV = *9999* ]]; then
 		git://github.com/gromacs/gromacs.git
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-6"
-	use hybrid && EGIT_BRANCH="nbnxn_hybrid_acc"
 	inherit git-2
+	PDEPEND="doc? ( ~app-doc/gromacs-manual-${PV} )"
 else
 	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
 fi
@@ -37,7 +35,7 @@ HOMEPAGE="http://www.gromacs.org/"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE="X blas cuda doc -double-precision +fftw gsl hybrid lapack
+IUSE="X blas cuda doc -double-precision +fftw gsl lapack
 mpi openmp +single-precision test +threads xml zsh-completion ${ACCE_IUSE}"
 
 CDEPEND="
@@ -56,12 +54,11 @@ CDEPEND="
 	xml? ( dev-libs/libxml2:2 )"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig"
-RDEPEND="${CDEPEND}
-	app-shells/tcsh"
+RDEPEND="${CDEPEND}"
 
 RESTRICT="test"
 
-REQUIRED_USE="cuda? ( !double-precision hybrid )"
+REQUIRED_USE="cuda? ( !double-precision )"
 
 pkg_pretend() {
 	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
@@ -121,9 +118,6 @@ src_configure() {
 	use avx128fma && acce="AVX_128_FMA"
 	use avx256 && acce="AVX_256"
 
-	#workaround for now
-	use sse2 && use hybrid && CFLAGS+=" -msse2"
-
 	#to create man pages, build tree binaries are executed (bug #398437)
 	[[ ${CHOST} = *-darwin* ]] && \
 		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
@@ -209,8 +203,11 @@ src_install() {
 	cd "${S}"
 	dodoc AUTHORS INSTALL* README*
 	if use doc; then
-		newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
 		dohtml -r "${ED}usr/share/gromacs/html/"
+		insinto /usr/share/gromacs
+		doins "admin/programs.txt"
+		ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
+		doins "${T}"/programs.list
 	fi
 	rm -rf "${ED}usr/share/gromacs/html/"
 }
@@ -225,9 +222,4 @@ pkg_postinst() {
 	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
 	einfo
 	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
-	if use hybrid; then
-		elog "Cuda and hybrid acceleration is still experimental,"
-		elog "use 'cutoff-scheme = Verlet' in your mdp file and"
-		elog "report bugs: http://redmine.gromacs.org/issues"
-	fi
 }
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index d74f3cd01..1e7bf0c9b 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -42,9 +42,8 @@ CDEPEND="
 	xml? ( dev-libs/libxml2:2 )"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig"
-RDEPEND="${CDEPEND}
-	app-shells/tcsh"
-PDEPEND="doc? ( app-doc/gromacs-manual )"
+RDEPEND="${CDEPEND}"
+PDEPEND="doc? ( ~app-doc/gromacs-manual-${PV} )"
 
 RESTRICT="test"
 
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index dd3f082b0..acbcd53ae 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -9,7 +9,6 @@
 	<use>
 		<flag name="cuda">Enable cuda non-bonded kernels</flag>
 		<flag name="double-precision">More precise calculations at the expense of speed</flag>
-		<flag name="hybrid">Enable hybrid acceleration kernels</flag>
 		<flag name="single-precision">Single precision version of gromacs (default)</flag>
 		<!-- acceleration optimization flags -->
 		<flag name="fkernels">Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
diff --git a/sci-chemistry/phenix-bin/ChangeLog b/sci-chemistry/phenix-bin/ChangeLog
new file mode 100644
index 000000000..22c887a87
--- /dev/null
+++ b/sci-chemistry/phenix-bin/ChangeLog
@@ -0,0 +1,23 @@
+# ChangeLog for sci-chemistry/phenix-bin
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  21 Sep 2012; Justin Lecher <jlec@gentoo.org> phenix-bin-1.8.1069.ebuild:
+  Add missing dep
+
+  21 Sep 2012; Justin Lecher <jlec@gentoo.org> phenix-bin-1.8.1069.ebuild:
+  Don't double prefix
+
+  21 Sep 2012; Justin Lecher <jlec@gentoo.org> phenix-bin-1.8.1069.ebuild:
+  Not everyone installs on my box
+
+  20 Sep 2012; Justin Lecher <jlec@gentoo.org> +phenix-bin-1.8.1069.ebuild,
+  +metadata.xml:
+  New Addition
+
+*phenix-bin-1.8.1069 (20 Sep 2012)
+
+  20 Sep 2012; Justin Lecher <jlec@gentoo.org> +phenix-bin-1.8.1069.ebuild,
+  +metadata.xml:
+  New Addition
+
diff --git a/sci-chemistry/phenix-bin/Manifest b/sci-chemistry/phenix-bin/Manifest
new file mode 100644
index 000000000..444122b38
--- /dev/null
+++ b/sci-chemistry/phenix-bin/Manifest
@@ -0,0 +1,2 @@
+DIST phenix-installer-1.8-1069-intel-linux-2.6-fc3.tar 624865280 SHA256 71effa3e58be1acc94687ae89c9350b7088883af1c71e533bdae1c426d1770db SHA512 352a964b8c5235ae9a8a7a051fb182bae45c4ef136d140014d8d415d9039bc55cb5625f98b8ac7ed3c6b1f49202cc46277d6757313659b655ebc681a6bfdcf0c WHIRLPOOL c00d79fd11af4caf958aad6e28b74547cdb81016ccc1c72998361c078a3e6fa5782eb562e104b2fdf11bff986e4596a04aca523f88dbcee1707ed3ac9a6c4388
+DIST phenix-installer-1.8-1069-intel-linux-2.6-x86_64-fc15.tar 632821760 SHA256 8b237a437043364bf39e3316931d895d3dd317823f9a98a01404eb424b5224cd SHA512 6160d5d85d1374c0b9c65cdd57c36c51b88cdb53af4341b567820d824727300403025da22de5619c8a6e742446dfe094f99e7727c5209338c33d6676876b91f2 WHIRLPOOL 70d2d3abd07f67094490d3307af31478c2236010473b1ed7f8ac1263c5f2da249640be0f99346bc6c5e8eb74acc9cce46a13cf76b530691125527e67ac302ac4
diff --git a/sci-chemistry/phenix-bin/metadata.xml b/sci-chemistry/phenix-bin/metadata.xml
new file mode 100644
index 000000000..d369d068f
--- /dev/null
+++ b/sci-chemistry/phenix-bin/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</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/phenix-bin/phenix-bin-1.8.1069.ebuild b/sci-chemistry/phenix-bin/phenix-bin-1.8.1069.ebuild
new file mode 100644
index 000000000..fa7088c6f
--- /dev/null
+++ b/sci-chemistry/phenix-bin/phenix-bin-1.8.1069.ebuild
@@ -0,0 +1,87 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+PYTHON_DEPEND="2"
+
+inherit python versionator
+
+MY_PV="$(replace_version_separator 2 -)"
+MY_P="phenix-installer-${MY_PV}"
+
+DESCRIPTION="Python-based Hierarchical ENvironment for Integrated Xtallography"
+HOMEPAGE="http://phenix-online.org/"
+SRC_URI="
+	amd64? ( phenix-installer-${MY_PV}-intel-linux-2.6-x86_64-fc15.tar )
+	x86? ( phenix-installer-${MY_PV}-intel-linux-2.6-fc3.tar )
+"
+
+SLOT="0"
+LICENSE="phenix"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	media-libs/jpeg:62"
+DEPEND=""
+
+RESTRICT="fetch"
+
+QA_PREBUILT="opt/phenix-${MY_PV}/.*"
+
+S="${WORKDIR}"/${MY_P}
+
+pkg_nofetch() {
+	elog "Please visit"
+	elog "http://www.phenix-online.org/phenix_request/index.cgi"
+	elog "and request a download password. With that done,"
+	elog "visit http://www.phenix-online.org/download/phenix/release"
+	elog "and downlaod ${A} to ${DISTDIR}"
+}
+
+pkg_setup() {
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_prepare() {
+	./install --prefix="${S}/foo"
+
+}
+
+src_install() {
+#	find -name "*.py[co]" -delete
+#	find -name SConstruct -delete
+	sed \
+		-e "s:${S}/foo:${EPREFIX}/opt:g" \
+		-i \
+			build-binary/intel-linux-2.6-*/*/log/*.log \
+			build-final/intel-linux-2.6-*/*/log/*.log \
+			foo/phenix-${MY_PV}/build/intel-linux-2.6-*/*_env \
+			foo/phenix-${MY_PV}/build/intel-linux-*/*sh \
+			foo/phenix-${MY_PV}/build/intel-linux-*/bin/* \
+			foo/phenix-${MY_PV}/build/intel-linux-2.6-*/base/etc/{gtk*,pango}/* \
+			foo/phenix-${MY_PV}/phenix_env* \
+			|| die
+#	grep ${S} * -R
+	dodir /opt
+	mv "${S}/foo/phenix-${MY_PV}" "${ED}/opt/"
+
+	cat >> phenix <<- EOF
+	#!${EPREFIX}/bin/bash
+
+	source "${EPREFIX}/opt/phenix-${MY_PV}/phenix_env.sh"
+	exec phenix
+	EOF
+	dobin phenix
+}
+
+pkg_postinst() {
+	python_mod_optimize "/opt/phenix-${MY_PV}"
+}
+
+pkg_postrm() {
+	python_mod_cleanup "/opt/phenix-${MY_PV}"
+}
diff --git a/sci-chemistry/specView/ChangeLog b/sci-chemistry/specView/ChangeLog
new file mode 100644
index 000000000..ed8647ed7
--- /dev/null
+++ b/sci-chemistry/specView/ChangeLog
@@ -0,0 +1,19 @@
+# ChangeLog for sci-chemistry/specView
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  21 Sep 2012; Justin Lecher <jlec@gentoo.org> specView-1.0.2.ebuild:
+  Needs webkit support in pyside
+
+  21 Sep 2012; Justin Lecher <jlec@gentoo.org> specView-1.0.2.ebuild:
+  Prefix offset for header dirs
+
+  21 Sep 2012; Justin Lecher <jlec@gentoo.org> specView-1.0.2.ebuild:
+  Copile py code
+
+*specView-1.0.2 (21 Sep 2012)
+
+  21 Sep 2012; Justin Lecher <jlec@gentoo.org> +specView-1.0.2.ebuild,
+  +files/specView, +metadata.xml:
+  New addition
+
diff --git a/sci-chemistry/specView/Manifest b/sci-chemistry/specView/Manifest
new file mode 100644
index 000000000..9ad3c9159
--- /dev/null
+++ b/sci-chemistry/specView/Manifest
@@ -0,0 +1 @@
+DIST specView1.0.2.tar.gz 15811413 SHA256 3a8d8b9e0f15e6481d8d6ea9a1f51d06a3cd2a4295acc3dfaf9e4ee0e3b1509f SHA512 f3194148f90d9dbe706c33fefda9cb6db71e0812f83bbf94bb170170bd9d4fcd4eae6295ccc78c6544b093dfbf09512555405dfab5b0516152dce2cb25b18965 WHIRLPOOL d35dd8753565f29b36c55014b8b34f0a5c60fad9f4353d4a094b6a7d2010a9936e9e3e42d27c4d5e6076a861fe7eb424acf86c7847e0218e8877ffb4a9865411
diff --git a/sci-chemistry/specView/files/specView b/sci-chemistry/specView/files/specView
new file mode 100644
index 000000000..bca546ca7
--- /dev/null
+++ b/sci-chemistry/specView/files/specView
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+export CCPNMR_TOP_DIR=gentoo_sitedir
+export PYTHONPATH=.:${CCPNMR_TOP_DIR}/specView/python
+export LD_LIBRARY_PATH=gentoolibdir
+export TCL_LIBRARY=gentootcl
+export TK_LIBRARY=gentootk
+export PSIPRED_DIR=gentoousr
+gentoopython -O ${CCPNMR_TOP_DIR}/specView/python/ccpnmr/specView/SpecView.py $@
diff --git a/sci-chemistry/specView/metadata.xml b/sci-chemistry/specView/metadata.xml
new file mode 100644
index 000000000..d369d068f
--- /dev/null
+++ b/sci-chemistry/specView/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</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/specView/specView-1.0.2.ebuild b/sci-chemistry/specView/specView-1.0.2.ebuild
new file mode 100644
index 000000000..f435c6067
--- /dev/null
+++ b/sci-chemistry/specView/specView-1.0.2.ebuild
@@ -0,0 +1,108 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+PYTHON_DEPEND="2"
+
+inherit python toolchain-funcs
+
+DESCRIPTION="Fast way to visualise NMR spectrum and peak data"
+HOMEPAGE="http://www.ccpn.ac.uk/software/specview"
+SRC_URI="http://www2.ccpn.ac.uk/download/ccpnmr/${PN}${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	dev-python/pyopengl
+	dev-python/pyside[webkit]"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/ccpnmr/ccpnmr3.0/
+
+#TODO:
+#install in sane place
+#unbundle data model
+#unbundle inchi
+#parallel build
+
+pkg_setup() {
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_prepare() {
+	sed \
+		-e "s|/usr|${EPREFIX}/usr|g" \
+		-e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
+		-e '/^MALLOC_FLAG/s:^:#:g' \
+		-e "/^OPT_FLAG/s:=.*$:= ${CFLAGS}:g" \
+		-e "/^LINK_FLAGS/s:$: ${LDFLAGS}:g" \
+		-e "/^PYTHON_DIR/s:=.*:= ${EPREFIX}/usr:g" \
+		-e "/^PYTHON_LIB/s:=.*:= $(python_get_library -l):g" \
+		-e "/^PYTHON_INCLUDE_FLAGS/s:=.*:= -I${EPREFIX}$(python_get_includedir) -I${EPREFIX}$(python_get_sitedir)/numpy/core/include/numpy:g" \
+		-e "/^PYTHON_LIB_FLAGS/s:=.*:= -L${EPREFIX}/usr/$(get_libdir):g" \
+		-e "/^SHARED_FLAGS/s:=.*:= -shared:g" \
+		-e "/^GL_DIR/s:=.*:= ${EPREFIX}/usr/$(get_libdir):g" \
+		-e "/^GL_INCLUDE_FLAGS/s:=.*:= -I${EPREFIX}/usr/include:g" \
+		-e "/^GL_LIB_FLAGS/s:=.*:= -L${EPREFIX}/usr/$(get_libdir):g" \
+		cNg/environment_default.txt > cNg/environment.txt || die
+	echo "SHARED_LINK_PARM = ${LDFLAGS}" >> cNg/environment.txt || die
+
+	rm -rf license || die
+
+	sed \
+	-e 's:ln -s:cp -f:g' \
+	-i $(find python -name linkSharedObjs) || die
+}
+
+src_compile() {
+	emake -C cNg all
+	emake -j1 -C cNg links
+}
+
+src_install() {
+	local in_path=$(python_get_sitedir)/${PN}
+	local _file
+
+	find . -name "*.pyc" -type f -delete
+	dodir /usr/bin
+	sed \
+	-e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
+	-e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
+	-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
+	-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
+	-e "s|gentoopython|$(PYTHON -a)|g" \
+	-e "s|gentoousr|${EPREFIX}/usr|g" \
+	-e "s|//|/|g" \
+		"${FILESDIR}"/${PN} > "${ED}"/usr/bin/${PN} || die
+	fperms 755 /usr/bin/${PN}
+
+	insinto ${in_path}
+
+	dodir ${in_path}/cNg
+	rm -rf cNg || die
+
+	ebegin "Installing main files"
+		doins -r *
+	eend
+
+	ebegin "Adjusting permissions"
+
+	for _file in $(find "${ED}" -type f -name "*so"); do
+		chmod 755 ${_file}
+	done
+	eend
+}
+
+pkg_postinst() {
+	python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup ${PN}
+}