vmd: add patch to include thrust/device_ptr (CUDA 5.5)

6 files changed, 551 insertions, 0 deletions

diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
new file mode 100644
index 0000000..43b27be
--- /dev/null
+++ b/sci-chemistry/vmd/ChangeLog
@@ -0,0 +1,261 @@
+# ChangeLog for sci-chemistry/vmd
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.56 2013/03/01 08:23:03 jlec Exp $
+
+  01 Mar 2013; Justin Lecher <jlec@gentoo.org> vmd-1.9.1.ebuild,
+  vmd-1.9.1-r1.ebuild, vmd-1.9.1-r2.ebuild:
+  Fix tcl/tk API to version 8.5, #451824; Upstream says it will be fixed in
+  version 1.9.2
+
+  24 Jan 2013; Justin Lecher <jlec@gentoo.org> vmd-1.9.1.ebuild,
+  vmd-1.9.1-r1.ebuild:
+  Force py2, #450716
+
+
+  18 Jan 2013; Christoph Junghans <ottxor@gentoo.org> vmd-1.9.1-r2.ebuild:
+  fix deps
+
+*vmd-1.9.1-r2 (11 Jan 2013)
+
+  11 Jan 2013; Justin Lecher <jlec@gentoo.org> +vmd-1.9.1-r2.ebuild,
+  +files/vmd-1.9.1-tcl8.6.patch, metadata.xml:
+  Use cuda.eclass and slo-operator for tcl
+
+  29 Nov 2012; Justin Lecher <jlec@gentoo.org> vmd-1.9.1.ebuild,
+  vmd-1.9.1-r1.ebuild:
+  Drop dep on old tk
+
+  15 Nov 2012; Christoph Junghans <ottxor@gentoo.org> vmd-1.9.1-r1.ebuild:
+  fix build on x86
+
+*vmd-1.9.1-r1 (14 Nov 2012)
+
+  14 Nov 2012; Justin Lecher <jlec@gentoo.org> +vmd-1.9.1-r1.ebuild:
+  Fix detection of netcdf; #406737, thanks Reinis Danne preparing the patch;
+  Loosen dep for cuda support, #406083
+
+  24 Sep 2012; Mike Frysinger <vapier@gentoo.org> vmd-1.9.1.ebuild:
+  QA_DT_HASH (old/deprecated) -> QA_FLAGS_IGNORED (new hotness).
+
+  05 Sep 2012; Justin Lecher <jlec@gentoo.org> -vmd-1.8.7-r2.ebuild,
+  -vmd-1.9.ebuild, vmd-1.9.1.ebuild:
+  Bumped to EAPI=4; use domenu; drop old
+
+  14 Feb 2012; Alexey Shvetsov <alexxy@gentoo.org> vmd-1.9.1.ebuild:
+  Fix plugin install
+
+*vmd-1.9.1 (14 Feb 2012)
+
+  14 Feb 2012; Alexey Shvetsov <alexxy@gentoo.org> +vmd-1.9.1.ebuild:
+  Version bump =D
+
+  10 Jan 2012; Justin Lecher <jlec@gentoo.org> vmd-1.9.ebuild:
+  Remove USE=static-libs because this breaks build, #365051
+
+  10 Jan 2012; Justin Lecher <jlec@gentoo.org> vmd-1.9.ebuild, metadata.xml:
+  Enhance nofetch msg, fix compilation with USE=cuda and gcc != 4.4*, thanks
+  xarthisius for the help
+
+  20 Jul 2011; Pacho Ramos <pacho@gentoo.org> metadata.xml:
+  Drop maintainer due retirement, bug #105599
+
+  15 Jun 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild,
+  vmd-1.9.ebuild:
+  FILESDIR is gone, wverything is mirrored now.
+
+  13 Jun 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild,
+  vmd-1.9.ebuild:
+  Mirrored files aren't fetchrestricted
+
+  13 Jun 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild,
+  -files/vmd-1.8.7-gentoo.patch, -files/vmd-1.8.7-respect-flags.patch,
+  vmd-1.9.ebuild, -files/vmd-1.9-gentoo-base.patch,
+  -files/vmd-1.9-gentoo-plugins.patch, -files/vmd.desktop, -files/vmd.png:
+  No binaryfiles in VCS please, #370915
+
+  27 Mar 2011; Justin Lecher <jlec@gentoo.org> vmd-1.9.ebuild:
+  Correct version of cuda dep, #360401
+
+*vmd-1.9 (22 Mar 2011)
+
+  22 Mar 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild,
+  +vmd-1.9.ebuild, +files/vmd-1.9-gentoo-base.patch,
+  +files/vmd-1.9-gentoo-plugins.patch, metadata.xml:
+  Version Bump, #358981; Dropped ppc due to missing KEYWORDS in DEPs
+
+  22 Mar 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild:
+  Restrict fltk version being able to return includedir
+
+  20 Mar 2011; Justin Lecher <jlec@gentoo.org> -vmd-1.8.7-r1.ebuild,
+  vmd-1.8.7-r2.ebuild:
+  x11-libs/fltk SLOTMOVE 1.1 -> 1, corrected ebuild accordingly
+
+  11 Dec 2010; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild:
+  QA on quoting
+
+  30 Oct 2010; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild:
+  Corrected msms DEP to sci-chemistry/msms-bin
+
+  21 Aug 2010; Alexey Shvetsov <alexxy@gentoo.org> vmd-1.8.7-r2.ebuild,
+  metadata.xml:
+  Add msms and povray to RDEPS as per bug #293504
+
+*vmd-1.8.7-r2 (27 Jul 2010)
+
+  27 Jul 2010; Justin Lecher <jlec@gentoo.org>
+  -files/vmd-1.8.5-config-gentoo.patch,
+  -files/vmd-1.8.6-config-gentoo.patch,
+  -files/vmd-1.8.6-fix-crash-on-tcl8.5.patch,
+  -files/vmd-1.8.6-python-2.5.patch, -files/vmd-1.8.6-tcltk8.5.patch,
+  vmd-1.8.7-r1.ebuild, +vmd-1.8.7-r2.ebuild, -files/vmd-1.8.7-config.patch,
+  files/vmd-1.8.7-gentoo.patch, +files/vmd-1.8.7-respect-flags.patch,
+  -files/vmd-1.8.7-use-bash-startup.patch:
+  Make it really prefix ready, don't mix CFLAGS/CXXFLAGS,clean old patches
+
+  24 Jul 2010; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r1.ebuild:
+  Added prefix changes, thanks rei4dan #327517; keyworded for ~-linux prefix
+
+  28 May 2010; Justin Lecher <jlec@gentoo.org> -vmd-1.8.6.ebuild,
+  -vmd-1.8.6-r1.ebuild, -vmd-1.8.7.ebuild:
+  Removed all non PythonABI compatible ebuilds
+
+*vmd-1.8.7-r1 (18 May 2010)
+
+  18 May 2010; Justin Lecher <jlec@gentoo.org> +vmd-1.8.7-r1.ebuild,
+  files/vmd-1.8.7-config.patch, +files/vmd-1.8.7-gentoo.patch:
+  Fix for new python ABIs, #316187; building netcdf plugin, #306893, thanks
+  Kamil Kisiel for the patch; LDFLAGS are respected now; EAPI=3 and basic
+  fixes for prefix, usability has to be tested
+
+  23 Feb 2010; Alexey Shvetsov <alexxy@gentoo.org> vmd-1.8.6-r1.ebuild,
+  vmd-1.8.7.ebuild, metadata.xml:
+  add tachyon raytracer as rdep
+
+  18 Sep 2009; Petteri Räty <betelgeuse@gentoo.org> vmd-1.8.7.ebuild:
+  Remove built_with_use and use proper DEPEND atoms that work properly for
+  both tk 8.4 and 8.5 users.
+
+  11 Aug 2009; Markus Dittrich <markusle@gentoo.org> vmd-1.8.7.ebuild,
+  +files/vmd.desktop, +files/vmd.png:
+  Added desktop entry and vmd icon (#262275).
+  Thanks much to Bjoern Olausson for creating them.
+
+  07 Aug 2009; Markus Dittrich <markusle@gentoo.org> vmd-1.8.7.ebuild,
+  files/vmd-1.8.7-config.patch:
+  Remove the EAPI2 check for -truetype and add explicit error logic
+  so tk-8.4 users can emerge vmd as well. Also updated the config
+  patch to handle tk8.4 better.
+
+*vmd-1.8.7 (05 Aug 2009)
+
+  05 Aug 2009; Markus Dittrich <markusle@gentoo.org> +vmd-1.8.7.ebuild,
+  +files/vmd-1.8.7-config.patch, +files/vmd-1.8.7-use-bash-startup.patch:
+  Version bump (fixes bug #262275).
+
+  07 Jul 2009; Diego E. Pettenò <flameeyes@gentoo.org> vmd-1.8.6-r1.ebuild:
+  Use elog for fetch error.
+
+  18 May 2009; Jeff Gardner <je_fro@gentoo.org>
+  +files/vmd-1.8.6-fix-crash-on-tcl8.5.patch:
+  adding alexxy's patch :)
+
+  17 May 2009; Jeff Gardner <je_fro@gentoo.org> +vmd-1.8.6-r1.ebuild:
+  Fixed by alexxy to work with tcl8.5
+
+*vmd-1.8.6-r1 (17 May 2009)
+
+  17 May 2009; Jeff Gardner <je_fro@gentoo.org> +vmd-1.8.6-r1.ebuild:
+  Fixed by alexxy to work with tcl5.8
+
+  12 Nov 2008; Markus Dittrich <markusle@gentoo.org> -vmd-1.8.5.ebuild,
+  vmd-1.8.6.ebuild:
+  Restrict fltk to 1.1 slot since vmd is not fltk-2 ready 
+  (see bug #246445). Removed old ebuild.
+
+  13 Mar 2008; Markus Dittrich <markusle@gentoo.org>
+  +files/vmd-1.8.6-tcltk8.5.patch, vmd-1.8.6.ebuild:
+  Added tcltk-8.5 support (fixes bug #212936).
+
+  20 Sep 2007; Markus Dittrich <markusle@gentoo.org>
+  +files/vmd-1.8.6-python-2.5.patch, vmd-1.8.6.ebuild:
+  Added patch to fix python-2.5 compile issues on amd64 (fixes bug
+  #192902). Thanks much to milan hodoscek <milan@cmm.ki.si> for his
+  patch.
+
+  22 Jul 2007; Donnie Berkholz <dberkholz@gentoo.org>; vmd-1.8.5.ebuild,
+  vmd-1.8.6.ebuild:
+  Drop virtual/x11 references.
+
+*vmd-1.8.6 (15 Apr 2007)
+
+  15 Apr 2007; Markus Dittrich <markusle@gentoo.org>
+  -files/vmd-1.8.4-config-gentoo.patch, -files/vmd-1.8.4-paratool.patch,
+  -files/vmd-1.8.4-plugin-autopsf.patch,
+  +files/vmd-1.8.6-config-gentoo.patch, +vmd-1.8.6.ebuild:
+  Version bump (fixes bug #174595). Thanks much to Jeffrey Gardner
+  <je_fro@gentoo.org> for his patch and ebuild.
+
+  08 Jan 2007; Danny van Dyk <kugelfang@gentoo.org> -vmd-1.8.4.ebuild,
+  -vmd-1.8.4-r1.ebuild:
+  QA: Removed unused versions.
+
+  07 Jan 2007; Markus Dittrich <markusle@gentoo.org> vmd-1.8.5.ebuild:
+  Replaced backslashes with colons in some sed statements 
+  (see bug #145467).
+
+  03 Jan 2007; Jeff Gardner <je_fro@gentoo.org> vmd-1.8.5.ebuild:
+  added ~amd64
+
+  27 Dec 2006; Markus Dittrich <markusle@gentoo.org> vmd-1.8.5.ebuild:
+  Remove netcdf use flag and enable netcdf support by default
+  since it is needed by the catdcd plugin. This fixes bug #159081.
+
+  22 Dec 2006; Markus Dittrich <markusle@gentoo.org>
+  files/vmd-1.8.5-config-gentoo.patch, vmd-1.8.5.ebuild:
+  Added netcdf support. This fixes bug #158771.
+
+  09 Nov 2006; Markus Dittrich <markusle@gentoo.org> vmd-1.8.5.ebuild:
+  Enabled IMD functionality. Thanks to Stephane Gagne 
+  <sgagne@rsvs.ulaval.ca> for pointing this out (see bug #154429).
+
+  20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
+  (#148281) Change herd to sci-chemistry from sci.
+
+*vmd-1.8.5 (26 Aug 2006)
+
+  26 Aug 2006; Markus Dittrich <markusle@gentoo.org>
+  -files/vmd-1.8.3-config-gentoo.patch,
+  +files/vmd-1.8.5-config-gentoo.patch, -vmd-1.8.3.ebuild,
+  +vmd-1.8.5.ebuild:
+  Version bump. Also removed some of the old ebuilds.
+
+*vmd-1.8.4-r1 (13 Aug 2006)
+
+  13 Aug 2006; Markus Dittrich <markusle@gentoo.org>
+  +files/vmd-1.8.4-paratool.patch, +vmd-1.8.4-r1.ebuild:
+  VMD now depends on stride in order to properly display secondary
+  structure information. Also patched a paratool plugin error under
+  tcl-8.4.13.
+
+  29 Apr 2006; Marien Zwart <marienz@gentoo.org> Manifest:
+  Fix SHA256 digests.
+
+*vmd-1.8.4 (18 Apr 2006)
+
+  18 Apr 2006; Markus Dittrich <markusle@gentoo.org>
+  +files/vmd-1.8.4-config-gentoo.patch,
+  +files/vmd-1.8.4-plugin-autopsf.patch, +vmd-1.8.4.ebuild:
+  Version bump.
+
+  21 Mar 2006; Donnie Berkholz <spyderous@gentoo.org>; vmd-1.8.3.ebuild:
+  Keyword ~ppc, and make changes to the wrapper script that may also fix amd64
+  and alpha.
+
+  14 Feb 2006; Markus Dittrich <markusle@gentoo.org> Manifest:
+  Fixed bogus .Chanlog.swp file entry in Manifest.
+
+*vmd-1.8.3 (10 Feb 2006)
+
+  10 Feb 2006; Markus Dittrich <markusle@gentoo.org>
+  +files/vmd-1.8.3-config-gentoo.patch, +metadata.xml, +vmd-1.8.3.ebuild:
+  Initial import.
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
new file mode 100644
index 0000000..f2b41e3
--- /dev/null
+++ b/sci-chemistry/vmd/Manifest
@@ -0,0 +1,2 @@
+DIST vmd-1.9.1-gentoo-patches-2.tar.xz 79212 SHA256 1249957baea6fc8d4c05b008362b185b0851d70c6eeed8fbd44d41e7e77f23a8 SHA512 b313ed92652a93647790d668bd71233708fec3e9cead8b13b31dee1277f5ef6f0e8844f563ad51bc320b83a3cda126f8ab74fe4147218c65b594ee5624b46057 WHIRLPOOL 51b8a1486c286c002d893ec4e3aa8301ec7da6b9f2de31e880c7f9523a006a06712adecd5329269c892764761da691a36e1d6e5a730fc1a32c751b7658b96903
+DIST vmd-1.9.1.src.tar.gz 30748110 SHA256 54aa88e03d86d763383e7b98592a152c9d68e78383e13af0dd2aca09b002491f SHA512 a54cb08e8a9ce801c2ca986f746bff0a041a25d5cffebc8d4af50813b6c05d04a3209a27830d580287230edaf3048a78923ae54bf367ab69c3d81388ab1787bd WHIRLPOOL 26d2a855c0768583cd45aed105fdd8f1ef59d59b8ce11c1903f5fc2008ea05989b8a32a0d817725e711613f8abfc22bb5301f20ea8d597efe9c7913790b25bb7
diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-thrust-include-device-ptr.patch b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-thrust-include-device-ptr.patch
new file mode 100644
index 0000000..d65e59c
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-thrust-include-device-ptr.patch
@@ -0,0 +1,24 @@
+diff --git a/vmd-1.9.1/src/CUDAMarchingCubes.cu b/vmd-1.9.1/src/CUDAMarchingCubes.cu
+index 5bfe7bf..36faaf0 100755
+--- a/vmd-1.9.1/src/CUDAMarchingCubes.cu
++++ b/vmd-1.9.1/src/CUDAMarchingCubes.cu
+@@ -45,6 +45,7 @@
+ #include "CUDAMarchingCubes.h"
+ #include <thrust/scan.h>
+ #include <thrust/functional.h>
++#include <thrust/device_ptr.h>
+ 
+ // The number of threads to use for triangle generation 
+ // (limited by shared memory size)
+diff --git a/vmd-1.9.1/src/CUDAQuickSurf.cu b/vmd-1.9.1/src/CUDAQuickSurf.cu
+index a21ebde..7d94a15 100755
+--- a/vmd-1.9.1/src/CUDAQuickSurf.cu
++++ b/vmd-1.9.1/src/CUDAQuickSurf.cu
+@@ -638,6 +638,7 @@ static void * cudadensitythread(void *voidparms) {
+ // and only considering bins of atoms that fall within that radius.
+ //
+ #include <thrust/sort.h> // need thrust sorting primitives
++#include <thrust/device_ptr.h> // need thrust sorting primitives
+ 
+ #define GRID_CELL_EMPTY 0xffffffff
+ 
diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-tcl8.6.patch b/sci-chemistry/vmd/files/vmd-1.9.1-tcl8.6.patch
new file mode 100644
index 0000000..0c3e45d
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.1-tcl8.6.patch
@@ -0,0 +1,25 @@
+ plugins/molfile_plugin/src/webpdbplugin.c | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/plugins/molfile_plugin/src/webpdbplugin.c b/plugins/molfile_plugin/src/webpdbplugin.c
+index 80b3bb9..78597f5 100644
+--- a/plugins/molfile_plugin/src/webpdbplugin.c
++++ b/plugins/molfile_plugin/src/webpdbplugin.c
+@@ -202,7 +202,7 @@ static void *open_file_read(const char *filename, const char *filetype,
+   sprintf(url, "http://www.rcsb.org/pdb/downloadFile.do?fileFormat=pdb&compression=NO&structureId=%s",filename);
+   sprintf(cmd, "set token [::http::geturl \"%s\"]", url);
+   if (Tcl_Eval(interp, cmd) != TCL_OK) {
+-    fprintf(stderr, "Error loading PDB: %s\n",interp->result);
++    fprintf(stderr, "Error loading PDB: %s\n",Tcl_GetStringResult(interp));
+     Tcl_DeleteInterp(interp);
+     return NULL;
+   } 
+@@ -211,7 +211,7 @@ static void *open_file_read(const char *filename, const char *filetype,
+   
+   result = Tcl_GetVar2(interp, (char *)"state", "body", TCL_GLOBAL_ONLY); 
+   if (!result) {
+-    fprintf(stderr, "Error loading PDB: %s\n", interp->result);
++    fprintf(stderr, "Error loading PDB: %s\n", Tcl_GetStringResult(interp));
+     Tcl_DeleteInterp(interp);
+     return NULL;
+   } 
diff --git a/sci-chemistry/vmd/metadata.xml b/sci-chemistry/vmd/metadata.xml
new file mode 100644
index 0000000..b9b5a06
--- /dev/null
+++ b/sci-chemistry/vmd/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer>
+    <email>alexxy@gentoo.org</email>
+    <name>Alexey Shvetsov</name>
+  </maintainer>
+  <herd>sci-chemistry</herd>
+  <use>
+    <flag name="msms">Add support for MSMS SAS calcualtion tool</flag>
+    <flag name="povray">Add support for povray raytracer for HQ	images</flag>
+    <flag name="tachyon">Add support for tachyon raytracer for HQ images</flag>
+    <flag name="cuda">Use nvidia cuda toolkit for speeding up computations</flag>
+  </use>
+</pkgmetadata>
diff --git a/sci-chemistry/vmd/vmd-1.9.1-r2.ebuild b/sci-chemistry/vmd/vmd-1.9.1-r2.ebuild
new file mode 100644
index 0000000..4db1288
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.1-r2.ebuild
@@ -0,0 +1,224 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.9.1-r2.ebuild,v 1.3 2013/03/01 08:23:03 jlec Exp $
+
+EAPI=5
+
+PYTHON_DEPEND="2"
+
+inherit cuda eutils multilib prefix python toolchain-funcs
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+SRC_URI="
+	http://dev.gentoo.org/~jlec/distifles/${P}-gentoo-patches-2.tar.xz
+	${P}.src.tar.gz"
+
+SLOT="0"
+LICENSE="vmd"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cuda msms povray tachyon xinerama"
+
+RESTRICT="fetch"
+
+# currently, tk-8.5* with USE=truetype breaks some
+# tk apps such as Sequence Viewer or Timeline.
+CDEPEND="
+	=dev-lang/tk-8.5*:0=[-truetype]
+	dev-lang/perl
+	dev-python/numpy
+	sci-libs/netcdf
+	virtual/opengl
+	>=x11-libs/fltk-1.1.10-r2:1
+	x11-libs/libXft
+	x11-libs/libXi
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+	xinerama? ( x11-libs/libXinerama )"
+DEPEND="${CDEPEND}
+	dev-lang/swig"
+RDEPEND="${CDEPEND}
+	sci-biology/stride
+	sci-chemistry/surf
+	x11-terms/xterm
+	msms? ( sci-chemistry/msms-bin )
+	povray? ( media-gfx/povray )
+	tachyon? ( media-gfx/tachyon )"
+
+VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
+# Binary only plugin!!
+QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
+QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
+
+pkg_nofetch() {
+	elog "Please download ${P}.src.tar.gz from"
+	elog "${VMD_DOWNLOAD}"
+	elog "after agreeing to the license and get"
+	elog "http://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches-2.tar.xz"
+	elog "Place both in ${DISTDIR}"
+}
+
+pkg_setup() {
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_prepare() {
+	use cuda && cuda_sanitize
+
+	cd "${WORKDIR}"/plugins
+
+	epatch \
+		"${WORKDIR}"/${P}-gentoo-plugins.patch \
+		"${FILESDIR}"/${P}-tcl8.6.patch
+
+	[[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile)
+
+	sed \
+		-e "s:CC = gcc:CC = $(tc-getCC):" \
+		-e "s:CXX = g++:CXX = $(tc-getCXX):" \
+		-e "s:COPTO =.*\":COPTO = -fPIC -o\":" \
+		-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o\":" \
+		-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
+		-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
+		-e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \
+		-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \
+		-e "s:-ltcl8.5:-ltcl:" \
+		-i Make-arch || die "Failed to set up plugins Makefile"
+
+	sed \
+		-e '/^AR /s:=:?=:g' \
+		-e '/^RANLIB /s:=:?=:g' \
+		-i ../plugins/*/Makefile || die
+
+	tc-export AR RANLIB
+
+	sed \
+		-e "s:\$(CXXFLAGS)::g" \
+		-i hesstrans/Makefile || die
+
+	# prepare vmd itself
+	cd "${S}"
+
+	epatch "${WORKDIR}"/${P}-gentoo-base.patch
+	epatch "${FILESDIR}"/${P}-cuda-thrust-include-device-ptr.patch
+
+	# PREFIX
+	sed \
+		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
+		-i configure || die
+
+	sed \
+		-e "s:gentoo-bindir:${ED}/usr/bin:g" \
+		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \
+		-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \
+		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:gentoo-gcc:$(tc-getCC):g" \
+		-e "s:gentoo-g++:$(tc-getCXX):g" \
+		-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \
+		-e "s:gentoo-cflags:${CFLAGS}:g" \
+		-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \
+		-e "s:gentoo-nvflags::g" \
+		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
+		-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
+		-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
+		-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \
+		-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \
+		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-i configure || die
+
+#	local NUMPY_INCLUDE="numpy/core/include"
+#	sed -e "s:gentoo-python-include:${EPREFIX}$(python_get_includedir):" \
+#		-e "s:gentoo-python-lib:${EPREFIX}$(python_get_libdir):" \
+#		-e "s:gentoo-python-link:$(PYTHON):" \
+#		-e "s:gentoo-numpy-include:${EPREFIX}$(python_get_sitedir)/${NUMPY_INCLUDE}:" \
+#		-i configure || die "failed setting up python"
+
+	if use cuda; then
+		sed \
+			-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
+			-e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
+			-i configure src/Makefile || die
+	fi
+
+	sed \
+		-e "s:LINUXPPC:LINUX:g" \
+		-e "s:LINUXALPHA:LINUX:g" \
+		-e "s:LINUXAMD64:LINUX:g" \
+		-e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \
+		-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \
+		-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \
+		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
+}
+
+src_configure() {
+	local myconf="OPENGL FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
+	rm -f configure.options && echo $myconf >> configure.options
+
+	use cuda && myconf+=" CUDA"
+#	use mpi && myconf+=" MPI"
+#	use tachion && myconf+=" LIBTACHYON"
+	use xinerama && myconf+=" XINERAMA"
+
+	export \
+		PYTHON_INCLUDE_DIR="${EPREFIX}$(python_get_includedir)" \
+		PYTHON_LIBRARY_DIR="${EPREFIX}$(python_get_libdir)" \
+		PYTHON_LIBRARY="$(python_get_library -l)" \
+		NUMPY_INCLUDE_DIR="${EPREFIX}$(python_get_sitedir)/numpy/core/include" \
+		NUMPY_LIBRARY_DIR="${EPREFIX}$(python_get_sitedir)/numpy/core/include"
+
+	./configure LINUX \
+		${myconf} || die
+}
+
+src_compile() {
+	# build plugins
+	cd "${WORKDIR}"/plugins
+
+	emake \
+		TCLINC="-I${EPREFIX}/usr/include" \
+		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" \
+		NETCDFLIB="$(pkg-config --libs-only-L netcdf) ${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" \
+		NETCDFINC="$(pkg-config --cflags-only-I netcdf) ${EPREFIX}/usr/include" \
+		NETCDFLDFLAGS="$(pkg-config --libs netcdf)" \
+		LINUX
+
+	# build vmd
+	cd "${S}"/src
+	emake
+}
+
+src_install() {
+	# install plugins
+	cd "${WORKDIR}"/plugins
+	emake \
+			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
+			distrib
+
+	# install vmd
+	cd "${S}"/src
+	emake install
+
+	# install docs
+	cd "${S}"
+	dodoc Announcement README doc/ig.pdf doc/ug.pdf
+
+	# remove some of the things we don't want and need in
+	# /usr/lib
+	cd "${ED}"/usr/$(get_libdir)/vmd
+	rm -fr doc README Announcement LICENSE || \
+		die "failed to clean up /usr/lib/vmd directory"
+
+	# adjust path in vmd wrapper
+	sed \
+		-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
+		-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
+		|| die "failed to set up vmd wrapper script"
+
+	# install icon and generate desktop entry
+	insinto /usr/share/pixmaps
+	doins "${WORKDIR}"/vmd.png
+	eprefixify "${WORKDIR}"/vmd.desktop
+	sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
+	domenu "${WORKDIR}"/vmd.desktop
+}