Squashed commit of the following:

commit 74c0e9192e17d9dfce50f811fdb7e82a2785134e
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Tue Oct 7 16:33:39 2008 +0200

    Merge

commit ad91fb07a47226ed9e99f2dcb55b69ea0e70aa84
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Tue Oct 7 16:23:20 2008 +0200

    openmotif: added some comments on license and download

commit 68a552975f5c7e0964c7c9625e08de0864757255
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Tue Oct 7 16:10:49 2008 +0200

    Match parameters so arb starts compiling against openmotif

commit 16c52fb4071193f89acf6f7f53cfeff322285555
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Tue Oct 7 16:04:06 2008 +0200

    Added openmotif package

commit 75c4bba418f16859e99e97f48785e27ad87e99f5
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Tue Oct 7 15:20:55 2008 +0200

    Adding openmotif

commit 83a847d194b007e2ef856f2a5ad7c49939b6cf8c
Merge: 52918f1... 5ba4f06...
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Tue Oct 7 14:15:05 2008 +0200

    Merge branch 'syncsvn'

    Conflicts:
    	pkgs/top-level/all-packages.nix

commit 52918f1f3af55429cc80c99d695e4a8d8b7869b0
Author: Pjotr Prins <wrk@nema-ws01.wurnet.nl>
Date:   Mon Oct 6 18:31:06 2008 +0200

    arb: Removed xfig as dependency (will add later)
    arb: Don't recurse chmod settings of shared dir

commit c283733782dcbf0dcd88710e83f3eededf8f0866
Merge: e434cdf... a51773a...
Author: Pjotr Prins <wrk@nema-ws01.wurnet.nl>
Date:   Mon Oct 6 17:09:42 2008 +0200

    Merge branch 'master' of ssh://bio4.xparrot.eu//export/data/repositories/git/nixpkgs-testing-pjotr

commit a51773a3d4295d7ce16e6a7e983ded814180e30a
Merge: 290ae0b... 241012c...
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Mon Oct 6 16:54:14 2008 +0200

    Merge branch 'master' of ssh://bio4.xparrot.eu//export/data/repositories/git/nixpkgs-testing-pjotr

commit e434cdf9b9acefab4f54e18204ff16af179c442d
Merge: ef57566... 241012c...
Author: Pjotr Prins <wrk@nema-ws01.wurnet.nl>
Date:   Mon Oct 6 16:12:27 2008 +0200

    Merge branch 'master' of ssh://bio4.xparrot.eu//export/data/repositories/git/nixpkgs-testing-pjotr

commit 241012cae194d0f770be2224b5bb18b66e3ae0f0
Author: Pj <wrk@bio03.(none)>
Date:   Mon Oct 6 16:11:11 2008 +0200

    Added older version of lesstif for arb

commit 290ae0b802285a8dda41b3c5730e53239d73b47c
Merge: dfdf7fe... 53b6ceb...
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Mon Oct 6 15:20:17 2008 +0200

    Merge branch 'master' of ssh://bio4.xparrot.eu//export/data/repositories/git/nixpkgs-testing-pjotr

commit dfdf7fe8ac9599ec372bdb83630a236f227ad7d5
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Mon Oct 6 15:15:04 2008 +0200

    Fixed missing parameters for arb - and added kernelHeaders_2.6.18

commit ef57566834eb786cdcb57a799b7d1cb284eee389
Author: Pjotr Prins <wrk@nema-ws01.wurnet.nl>
Date:   Mon Oct 6 15:06:26 2008 +0200

    Changed arb permissions and priority

svn path=/nixpkgs/trunk/; revision=12985

pkgs/applications/science/biology/arb/default.nix

@@ -13,7 +13,7 @@ stdenv.mkDerivation {
 
   patches = [ ./makefile.patch ];
 
-  buildInputs = [ glew mesa libpng libXpm lesstif lynx freeglut libtiff rxp sablotron libXaw perl jdk transfig libX11 libXext libXt gv xfig gnuplot ];
+  buildInputs = [ glew mesa libpng libXpm lesstif lynx freeglut libtiff rxp sablotron libXaw perl jdk transfig libX11 libXext libXt gv gnuplot ];
 
   unpackPhase = ''
     tar xzf $src
@@ -34,19 +34,19 @@ stdenv.mkDerivation {
     cp -vau lib/pts $shareddir/lib
     rm -vrf lib/pts
     ln -vs $shareddir/lib/pts $out/lib/pts
-    chmod a+rwx -R $shareddir/lib/pts
+    chmod a+rwx $shareddir/lib/pts
     # link out writable shared location lib/nas/
     ensureDir $shareddir/lib/nas
     cp -vau lib/nas $shareddir/lib
     rm -vrf lib/nas
     ln -vs $shareddir/lib/nas $out/lib/nas
-    chmod a+rwx -R $shareddir/lib/nas
+    chmod a+rwx $shareddir/lib/nas
     # link out shared lib/pixmaps (not sure about this, yet):
     ensureDir $shareddir/lib/pixmaps
     cp -vau lib/pixmaps $shareddir/lib
     rm -vrf lib/pixmaps
     ln -vs $shareddir/lib/pixmaps $out/lib/pixmaps
-    chmod a+rwx -R $shareddir/lib/pixmaps
+    chmod a+rwx $shareddir/lib/pixmaps
     # bulk copy
     cp -vau * $out
     # replace arb script

pkgs/development/libraries/openmotif/default.nix

@@ -0,0 +1,32 @@
+args: with args;
+
+# this is the stable edition of OpenMotif - sources fetched from Debian, without
+# patches applied
+
+stdenv.mkDerivation {
+  name = "openmotif-2.2.3";
+  src = fetchurl {
+    url = http://ftp.de.debian.org/debian/pool/non-free/o/openmotif/openmotif_2.2.3.orig.tar.gz; 
+    sha256 = "0amd9834p1ajnin7c8f1gad2jl2csf69msxcpc10rzm2x27jigxi";
+  };
+
+  unpackPhase = ''
+    tar xzf $src
+    tar xzf openmotif-2.2.3.orig/dist/openMotif-2.2.3.tar.gz
+    rm -rf openmotif-2.2.3.orig
+    cd openMotif-2.2.3
+  '';
+
+  buildInputs = [flex perl];
+  propagatedBuildInputs = [x11 libXp libXau libXaw libXext xbitmaps];
+
+  CFLAGS="-fno-strict-aliasing";  # without this openmotif may segfault
+
+  meta = {
+    description = "Open source version of motif toolkit including aka libmotif3";
+    homepage = http://www.opengroup.org/openmotif/;
+    # Open motif is free for open source projects
+    license = "non-free";
+  };
+}
+

pkgs/top-level/all-packages.nix

@@ -7361,7 +7361,7 @@ let
   arb = import ../applications/science/biology/arb {
     inherit fetchurl stdenv readline libpng zlib x11 lesstif93 freeglut perl;
     inherit (xlibs) libXpm libXaw libX11 libXext libXt;
-    inherit mesa glew libtiff lynx rxp sablotron jdk xfig transfig gv gnuplot;
+    inherit mesa glew libtiff lynx rxp sablotron jdk transfig gv gnuplot;
     lesstif = lesstif93;
   };