Merge from trunk up through r28790

svn path=/nixpkgs/branches/stdenv-updates/; revision=28792

28 files changed, 496 insertions, 360 deletions

diff --git a/pkgs/applications/science/astronomy/gravit/default.nix b/pkgs/applications/science/astronomy/gravit/default.nix
new file mode 100644
index 000000000000..8af963f84bc1
--- /dev/null
+++ b/pkgs/applications/science/astronomy/gravit/default.nix
@@ -0,0 +1,41 @@
+{ stdenv, fetchurl, SDL, SDL_ttf, SDL_image, mesa, lua5_0 }:
+
+let
+  name = "gravit-0.4.2";
+in
+stdenv.mkDerivation {
+  inherit name;
+
+  src = fetchurl {
+    url = "http://gravit.slowchop.com/dist/${name}.tar.gz";
+    sha256 = "f37f3ac256a4acbf575f709addaae8cb01eda4f85537affa28c45f2df6fddb07";
+  };
+
+  buildInputs = [mesa SDL SDL_ttf SDL_image lua5_0];
+
+  configureFlags = "CFLAGS=-O3 CXXFLAGS=-O3";
+
+  postInstall = ''
+    mv $out/etc/gravit $out/share/gravit/sample-config
+    rmdir $out/etc
+  '';
+
+  meta = {
+    homepage = "http://gravit.slowchop.com";
+    description = "A beautiful OpenGL-based gravity simulator";
+    license = "GPLv2";
+
+    longDescription = ''
+          Gravit is a gravity simulator which runs under Linux, Windows and
+      Mac OS X. It uses Newtonian physics using the Barnes-Hut N-body
+      algorithm. Although the main goal of Gravit is to be as accurate
+      as possible, it also creates beautiful looking gravity patterns.
+      It records the history of each particle so it can animate and
+      display a path of its travels. At any stage you can rotate your
+      view in 3D and zoom in and out.
+    '';
+
+    platforms = stdenv.lib.platforms.mesaPlatforms;
+    maintainers = [ stdenv.lib.maintainers.simons ];
+  };
+}
diff --git a/pkgs/applications/science/astronomy/stellarium/default.nix b/pkgs/applications/science/astronomy/stellarium/default.nix
new file mode 100644
index 000000000000..acf7721489a7
--- /dev/null
+++ b/pkgs/applications/science/astronomy/stellarium/default.nix
@@ -0,0 +1,31 @@
+{stdenv, fetchurl, cmake, freetype, libpng, mesa, gettext, openssl, qt4, perl, libiconv}:
+
+let
+  name = "stellarium-0.11.0";
+in
+stdenv.mkDerivation {
+  inherit name;
+
+  src = fetchurl {
+    url = "mirror://sourceforge/stellarium/${name}.tar.gz";
+    sha256 = "dbedf47dd0744fb325d67d63d1279101be7f4259af2a5e8027f1072012dd2587";
+  };
+
+  buildInputs = [ cmake freetype libpng mesa gettext openssl qt4 perl libiconv ];
+
+  cmakeFlags = "-DINTL_INCLUDE_DIR= -DINTL_LIBRARIES=";
+  preConfigure = ''
+    sed -i -e '/typedef void (\*__GLXextFuncPtr)(void);/d' src/core/external/GLee.h
+  '';
+
+  enableParallelBuilding = true;
+
+  meta = {
+    description = "an free open source planetarium";
+    homepage = http://stellarium.org/;
+    license = "GPL2";
+
+    platforms = stdenv.lib.platforms.linux; # should be mesaPlatforms, but we don't have qt on darwin
+    maintainers = [ stdenv.lib.maintainers.simons ];
+  };
+}
diff --git a/pkgs/applications/science/xplanet/default.nix b/pkgs/applications/science/astronomy/xplanet/default.nix
index 15e04c3835c3..15e04c3835c3 100644
--- a/pkgs/applications/science/xplanet/default.nix
+++ b/pkgs/applications/science/astronomy/xplanet/default.nix
diff --git a/pkgs/applications/science/chemistry/avogadro/default.nix b/pkgs/applications/science/chemistry/avogadro/default.nix
new file mode 100644
index 000000000000..702f4c28912f
--- /dev/null
+++ b/pkgs/applications/science/chemistry/avogadro/default.nix
@@ -0,0 +1,19 @@
+{ stdenv, fetchurl, cmake, qt4, zlib, eigen, openbabel }:
+
+stdenv.mkDerivation rec {
+  name = "avogadro-1.0.3";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/avogadro/${name}.tar.bz2";
+    sha256 = "0s44r78vm7hf4cs13d2qki3gf178gjj1ihph6rs04g6s4figvdpg";
+  };
+
+  buildInputs = [ qt4 eigen zlib openbabel ];
+
+  buildNativeInputs = [ cmake ];
+
+  meta = {
+    maintainers = [ stdenv.lib.maintainers.urkud ];
+    inherit (qt4.meta) platforms;
+  };
+}
diff --git a/pkgs/applications/science/electronics/gtkwave/default.nix b/pkgs/applications/science/electronics/gtkwave/default.nix
index 87a18c20e990..72c3f3e24356 100644
--- a/pkgs/applications/science/electronics/gtkwave/default.nix
+++ b/pkgs/applications/science/electronics/gtkwave/default.nix
@@ -1,10 +1,10 @@
 {stdenv, fetchurl, gtk, gperf, pkgconfig, bzip2, xz, tcl, tk, judy} :
 stdenv.mkDerivation rec {
-  name = "gtkwave-3.3.11";
+  name = "gtkwave-3.3.20";
 
   src = fetchurl {
     url = "mirror://sourceforge/gtkwave/${name}.tar.gz";
-    sha256 = "1krhxdpzj2ma3xisbk0d9yzhlk1i60hgkkfycc2nsqqirqrvdpbr";
+    sha256 = "0r2yh8a5rrxjzvykdmqlb098wws5c9k255saf2bsdchnigs8il3n";
   };
 
   buildInputs = [ gtk gperf pkgconfig bzip2 xz tcl tk judy];
diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix
index a804d9f84e6a..35395bd25d1e 100644
--- a/pkgs/applications/science/logic/coq/default.nix
+++ b/pkgs/applications/science/logic/coq/default.nix
@@ -4,7 +4,7 @@
 {stdenv, fetchurl, ocaml, findlib, camlp5, lablgtk, ncurses}:
 
 let
-  version = "8.3";
+  version = "8.3pl1";
 in
 
 stdenv.mkDerivation {
@@ -12,7 +12,7 @@ stdenv.mkDerivation {
 
   src = fetchurl {
     url = "http://coq.inria.fr/V${version}/files/coq-${version}.tar.gz";
-    sha256 = "02iy4rxz1n1kc85fb3vs4xpxqfxjw87y2gvmi39fxrj8742qx0dx";
+    sha256 = "0a791gsbf17y2wi0a376n78pxkhpl0lkzifhy5d3mx3lpn376j9s";
   };
 
   buildInputs = [ ocaml findlib camlp5 ncurses lablgtk ];
@@ -23,7 +23,7 @@ stdenv.mkDerivation {
     configureFlagsArray=(
       -camldir ${ocaml}/bin
       -camlp5dir $(ocamlfind query camlp5)
-      -lablgtkdir ${lablgtk}/lib/ocaml/lablgtk2 -opt -coqide opt
+      -lablgtkdir ${lablgtk}/lib/ocaml/*/site-lib/lablgtk2 -opt -coqide opt
     )
   '';
 
@@ -38,9 +38,12 @@ stdenv.mkDerivation {
     substituteInPlace tools/beautify-archive --replace "/bin/rm" "$RM"
     substituteInPlace scripts/coqmktop.ml --replace \
       "\"-I\"; \"+lablgtk2\"" \
-      "\"-I\"; \"${lablgtk}/lib/ocaml/lablgtk2\"; \"-I\"; \"${lablgtk}/lib/ocaml/stublibs\""
+      "\"-I\"; \"$(echo "${lablgtk}"/lib/ocaml/*/site-lib/lablgtk2)\"; \"-I\"; \"$(echo "${lablgtk}"/lib/ocaml/*/site-lib/stublibs)\""
   '';
 
+  # This post install step is needed to build ssrcoqide from the ssreflect package
+  # It could be made optional, but I see little harm in including it in the default
+  # distribution -- roconnor
   postInstall = ''
    cp ide/*.cmi ide/ide.*a $out/lib/coq/ide/
   '';
diff --git a/pkgs/applications/science/logic/hol_light/default.nix b/pkgs/applications/science/logic/hol_light/default.nix
index f923095f857e..d835e351cac6 100644
--- a/pkgs/applications/science/logic/hol_light/default.nix
+++ b/pkgs/applications/science/logic/hol_light/default.nix
@@ -1,43 +1,36 @@
-{stdenv, writeText, writeTextFile, ocaml, findlib, camlp5_transitional, hol_light_sources}:
+{stdenv, fetchsvn, writeScript, ocaml, findlib, camlp5}:
 
-let
-  version = hol_light_sources.version;
+stdenv.mkDerivation rec {
+  name = "hol_light-20110813";
+  src = fetchsvn {
+    url = http://hol-light.googlecode.com/svn/trunk;
+    rev = "102";
+    sha256 = "5b972672db6aa1838dc5d130accd9ab6a62030c6b0c1dc4b69e42088b1ae86c9";
+  };
 
-  camlp5 = camlp5_transitional;
+  buildInputs = [ ocaml findlib camlp5 ];
 
-  hol_light_src_dir = "${hol_light_sources}/lib/hol_light/src";
+  start_script = ''
+    #!/bin/sh
+    cd "$out/lib/hol_light"
+    exec ${ocaml}/bin/ocaml -I "$(ocamlfind query camlp5)" -init make.ml
+  '';
 
-  pa_j_cmo = stdenv.mkDerivation {
-    name = "pa_j.cmo";
-    inherit ocaml camlp5; 
-    buildInputs = [ ocaml camlp5 findlib ];
-    buildCommand = ''
-      ocamlc -c \
-        -pp "camlp5r pa_lexer.cmo pa_extend.cmo q_MLast.cmo" \
-        -I "$(ocamlfind query camlp5)" \
-        -o $out \
-        "${hol_light_src_dir}/pa_j_`ocamlc -version | cut -c1-4`.ml"
-      '';
-    };
+  buildPhase = ''
+    make pa_j.ml
+    ocamlc -c \
+      -pp "camlp5r pa_lexer.cmo pa_extend.cmo q_MLast.cmo" \
+      -I "$(ocamlfind query camlp5)" \
+      pa_j.ml
+  '';
 
-  start_ml = writeText "start.ml" ''
-    Topdirs.dir_directory "${hol_light_src_dir}";;
-    Topdirs.dir_directory ("${camlp5}/lib/ocaml/"^Sys.ocaml_version^"/site-lib/camlp5");;
-    Topdirs.dir_load Format.std_formatter "camlp5o.cma";;
-    Topdirs.dir_load Format.std_formatter "${pa_j_cmo}";;
-    #use "${hol_light_src_dir}/make.ml";;
+  installPhase = ''
+    ensureDir "$out/lib/hol_light" "$out/bin"
+    cp -a  . $out/lib/hol_light
+    echo "${start_script}" > "$out/bin/hol_light"
+    chmod a+x "$out/bin/hol_light"
   '';
-in
-writeTextFile {
-  name = "hol_light-${version}";
-  destination = "/bin/start_hol_light";
-  executable = true;
-  text = ''
-      #!/bin/sh
-      exec ${ocaml}/bin/ocaml -init ${start_ml}
-    '';
-} // {
-  inherit (hol_light_sources) version src;
+
   meta = {
     description = "An interactive theorem prover based on Higher-Order Logic.";
     longDescription = ''
diff --git a/pkgs/applications/science/logic/hol_light/dmtcp_checkpoint.nix b/pkgs/applications/science/logic/hol_light/dmtcp_checkpoint.nix
deleted file mode 100644
index 9071d63c298a..000000000000
--- a/pkgs/applications/science/logic/hol_light/dmtcp_checkpoint.nix
+++ /dev/null
@@ -1,99 +0,0 @@
-{stdenv, writeTextFile, hol_light, dmtcp}:
-let
-  mkRestartScript = checkpointFile:
-    let filename = "hol_light_${checkpointFile.variant}_dmtcp"; in
-    writeTextFile {
-      name = "${filename}-${hol_light.version}";
-      destination = "/bin/${filename}";
-      executable = true;
-      text = ''
-        #!/bin/sh
-	exec ${dmtcp}/bin/dmtcp_restart --quiet ${checkpointFile}
-      '';
-    };
-
-  mkCkptFile =
-    { variant
-    , banner
-    , loads
-    , startCkpt ? null
-    , buildCommand ? ''
-        cp ${startCkpt} hol_light_restart.ckpt
-        (echo "$loadScript" | dmtcp_restart --quiet hol_light_restart.ckpt) || exit 0
-        cp hol_light_restart.ckpt $out
-      ''
-    }:
-    stdenv.mkDerivation rec {
-      name = "hol_light_${variant}_dmtcp.checkpoint-${hol_light.version}";
-      inherit variant banner buildCommand;
-      buildInputs = [ dmtcp hol_light ];
-      loadScript = ''
-        ${loads}
-        dmtcp_checkpoint "${banner}";;
-      '';
-    };
-in
-rec {
-  hol_light_core_dmtcp = mkRestartScript hol_light_core_dmtcp_ckpt;
-  hol_light_sosa_dmtcp = mkRestartScript hol_light_sosa_dmtcp_ckpt;
-  hol_light_card_dmtcp = mkRestartScript hol_light_card_dmtcp_ckpt;
-  hol_light_multivariate_dmtcp = mkRestartScript hol_light_multivariate_dmtcp_ckpt;
-  hol_light_complex_dmtcp = mkRestartScript hol_light_complex_dmtcp_ckpt;
-
-  hol_light_core_dmtcp_ckpt = mkCkptFile rec {
-    variant = "core";
-    banner = "";
-    loads = ''
-      #use "${./dmtcp_selfdestruct.ml}";;
-    '';
-    buildCommand = ''
-      (echo "$loadScript" | dmtcp_checkpoint --quiet ${hol_light}/bin/start_hol_light) || exit 0
-      mv ckpt* $out
-    '';
-  };
-
-  hol_light_multivariate_dmtcp_ckpt = mkCkptFile {
-    variant = "multivariate";
-    banner = "Preloaded with multivariate analysis";
-    loads = ''
-      loadt "Multivariate/make.ml";;
-    '';
-    startCkpt = hol_light_core_dmtcp_ckpt;
-  };
-
-  hol_light_sosa_dmtcp_ckpt = mkCkptFile {
-    variant = "sosa";
-    banner = "Preloaded with analysis and SOS";
-    loads = ''
-      loadt "Library/analysis.ml";;
-      loadt "Library/transc.ml";;
-      loadt "Examples/sos.ml";;
-      loadt "update_database.ml";;
-    '';
-    startCkpt = hol_light_core_dmtcp_ckpt;
-  };
-
-  hol_light_card_dmtcp_ckpt = mkCkptFile {
-    variant = "card";
-    banner = "Preloaded with cardinal arithmetic";
-    loads = ''
-      loadt "Library/card.ml";;
-      loadt "update_database.ml";;
-    '';
-    startCkpt = hol_light_core_dmtcp_ckpt;
-  };
-
-  hol_light_complex_dmtcp_ckpt = mkCkptFile {
-    variant = "complex";
-    banner = "Preloaded with multivariate-based complex analysis";
-    loads = ''
-      loadt "Multivariate/complexes.ml";;
-      loadt "Multivariate/canal.ml";;
-      loadt "Multivariate/transcendentals.ml";;
-      loadt "Multivariate/realanalysis.ml";;
-      loadt "Multivariate/cauchy.ml";;
-      loadt "Multivariate/complex_database.ml";;
-    '';
-    startCkpt = hol_light_multivariate_dmtcp_ckpt;
-  };
-}
diff --git a/pkgs/applications/science/logic/hol_light/dmtcp_selfdestruct.ml b/pkgs/applications/science/logic/hol_light/dmtcp_selfdestruct.ml
deleted file mode 100644
index f85a7a6c5fdf..000000000000
--- a/pkgs/applications/science/logic/hol_light/dmtcp_selfdestruct.ml
+++ /dev/null
@@ -1,19 +0,0 @@
-(* ------------------------------------------------------------------------- *)
-(* Create a standalone HOL image. Assumes that we are running under Linux    *)
-(* and have the program "dmtcp" available to create checkpoints.             *)
-(* ------------------------------------------------------------------------- *)
-
-let dmtcp_checkpoint, dmtcp_selfdestruct =
-  let call_dmtcp opts bannerstring =
-    let longer_banner = startup_banner ^ " with DMTCP" in
-    let complete_banner =
-      if bannerstring = "" then longer_banner
-      else longer_banner^"\n        "^bannerstring in
-    (Gc.compact(); Unix.sleep 1;
-     Format.print_string "Checkpointing..."; Format.print_newline();
-     try ignore(Unix.system ("dmtcp_command -bc " ^ opts))
-     with Unix.Unix_error _ -> ();
-     Format.print_string complete_banner;
-     Format.print_newline(); Format.print_newline())
-  in
-  call_dmtcp "", call_dmtcp "-q";;
diff --git a/pkgs/applications/science/logic/hol_light/parser_setup.patch b/pkgs/applications/science/logic/hol_light/parser_setup.patch
deleted file mode 100644
index 0ad17ca1a0b0..000000000000
--- a/pkgs/applications/science/logic/hol_light/parser_setup.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-diff -Nuar hol_light/hol.ml hol_light.nixos/hol.ml
---- hol_light/hol.ml	2010-11-03 23:09:01.000000000 +0100
-+++ hol_light.nixos/hol.ml	2010-11-03 23:10:31.000000000 +0100
-@@ -11,8 +11,8 @@
- 
- let hol_version = "2.20++";;
- 
--let hol_dir = ref
--  (try Sys.getenv "HOLLIGHT_DIR" with Not_found -> Sys.getcwd());;
-+let hol_dir = ref "@HOL_LIGHT_SRC_DIR@";;
-+Topdirs.dir_directory "@HOL_LIGHT_SRC_DIR@";;
- 
- (* ------------------------------------------------------------------------- *)
- (* Should eventually change to "ref(Filename.temp_dir_name)".                *)
-@@ -23,19 +23,6 @@
- let temp_path = ref "/tmp";;
- 
- (* ------------------------------------------------------------------------- *)
--(* Load in parsing extensions.                                               *)
--(* For Ocaml < 3.10, use the built-in camlp4                                 *)
--(* and for Ocaml >= 3.10, use camlp5 instead.                                *)
--(* ------------------------------------------------------------------------- *)
--
--if let v = String.sub Sys.ocaml_version 0 4 in v >= "3.10"
--then (Topdirs.dir_directory "+camlp5";
--      Topdirs.dir_load Format.std_formatter "camlp5o.cma")
--else (Topdirs.dir_load Format.std_formatter "camlp4o.cma");;
--
--Topdirs.dir_load Format.std_formatter (Filename.concat (!hol_dir) "pa_j.cmo");;
--
--(* ------------------------------------------------------------------------- *)
- (* Load files from system and/or user-settable directories.                  *)
- (* Paths map initial "$/" to !hol_dir dynamically; use $$ to get the actual  *)
- (* $ character at the start of a directory.                                  *)
diff --git a/pkgs/applications/science/logic/hol_light/sources.nix b/pkgs/applications/science/logic/hol_light/sources.nix
deleted file mode 100644
index b45ca4a90349..000000000000
--- a/pkgs/applications/science/logic/hol_light/sources.nix
+++ /dev/null
@@ -1,28 +0,0 @@
-{stdenv, fetchsvn}:
-
-stdenv.mkDerivation rec {
-  name = "hol_light_sources-${version}";
-  version = "20101029";
-
-  src = fetchsvn {
-    url = http://hol-light.googlecode.com/svn/trunk;
-    rev = "64";
-    sha256 = "91e9cac62586039b13c11af245f85a743e299892b24b39d3c7b2ee13157e87c9";
-  };
-
-  buildCommand = ''
-    export HOL_DIR="$out/lib/hol_light"
-    ensureDir "$HOL_DIR"
-    cp -a "${src}" "$HOL_DIR/src"
-    cd "$HOL_DIR/src"
-    chmod +wX -R .
-    patch -p1 < ${./parser_setup.patch}
-    substituteInPlace hol.ml --subst-var-by HOL_LIGHT_SRC_DIR "$HOL_DIR/src"
-  '';
-
-  meta = {
-    description = "Sources for the HOL Light theorem prover";
-    homepage = http://www.cl.cam.ac.uk/~jrh13/hol-light/;
-    license = "BSD";
-  };
-}
diff --git a/pkgs/applications/science/logic/isabelle/default.nix b/pkgs/applications/science/logic/isabelle/default.nix
index b9e756e0423b..5705262f3771 100644
--- a/pkgs/applications/science/logic/isabelle/default.nix
+++ b/pkgs/applications/science/logic/isabelle/default.nix
@@ -3,7 +3,7 @@
 
 let
   pname = "Isabelle";
-  version = "2009-2";
+  version = "2011";
   name = "${pname}${version}";
   theories = ["HOL" "FOL" "ZF"];
 in
@@ -13,7 +13,7 @@ stdenv.mkDerivation {
 
   src = fetchurl {
     url = "http://www.cl.cam.ac.uk/research/hvg/${pname}/dist/${name}.tar.gz";
-    sha256 = "f92a275b78bd8844de47a5902e339b58f3b768c07a7fb19d8e606b68499d5ac4";
+    sha256 = "ea85eb2a859891be387f020b2e45f8c9a0bd1d8bbc3902f28a429e9c61cb0b6a";
   };
 
   buildInputs = [ perl polyml nettools ];
diff --git a/pkgs/applications/science/logic/isabelle/settings.patch b/pkgs/applications/science/logic/isabelle/settings.patch
index dc9c611d4886..bf509a4bac46 100644
--- a/pkgs/applications/science/logic/isabelle/settings.patch
+++ b/pkgs/applications/science/logic/isabelle/settings.patch
@@ -1,34 +1,32 @@
-diff -Naur Isabelle2009-1/etc/settings Isabelle2009-1-patched/etc/settings
---- Isabelle2009-1/etc/settings	2009-12-02 12:04:07.000000000 +0100
-+++ Isabelle2009-1-patched/etc/settings	2009-12-04 16:15:40.000000000 +0100
-@@ -16,15 +16,8 @@
- # Only one of the sections below should be activated.
+diff -Nuar Isabelle2011/etc/settings Isabelle2011-fix/etc/settings
+--- Isabelle2011/etc/settings	2011-01-30 13:02:18.000000000 +0100
++++ Isabelle2011-fix/etc/settings	2011-05-14 22:56:04.000000000 +0200
+@@ -17,13 +17,7 @@
  
  # Poly/ML 5.x (automated settings)
--POLY_HOME="$(type -p poly)"; [ -n "$POLY_HOME" ] && POLY_HOME="$(dirname "$POLY_HOME")"
  ML_PLATFORM="$ISABELLE_PLATFORM"
--ML_HOME=$(choosefrom \
+-ML_HOME="$(choosefrom \
 -  "$ISABELLE_HOME/contrib/polyml/$ML_PLATFORM" \
 -  "$ISABELLE_HOME/../polyml/$ML_PLATFORM" \
 -  "/usr/local/polyml/$ML_PLATFORM" \
 -  "/usr/share/polyml/$ML_PLATFORM" \
 -  "/opt/polyml/$ML_PLATFORM" \
--  $POLY_HOME)
+-  "")"
 +ML_HOME=@ML_HOME@
  ML_SYSTEM=$("$ISABELLE_HOME/lib/scripts/polyml-version")
  ML_OPTIONS="-H 200"
  ML_SOURCES="$ML_HOME/../src"
-@@ -185,13 +178,7 @@
+@@ -175,13 +169,7 @@
  ###
  
  # Proof General home, look in a variety of places
--PROOFGENERAL_HOME=$(choosefrom \
+-PROOFGENERAL_HOME="$(choosefrom \
 -  "$ISABELLE_HOME/contrib/ProofGeneral" \
 -  "$ISABELLE_HOME/../ProofGeneral" \
 -  "/usr/local/ProofGeneral" \
 -  "/usr/share/ProofGeneral" \
 -  "/opt/ProofGeneral" \
--  "")
+-  "")"
 +PROOFGENERAL_HOME=@PROOFGENERAL_HOME@
  
  PROOFGENERAL_OPTIONS=""
diff --git a/pkgs/applications/science/logic/leo2/default.nix b/pkgs/applications/science/logic/leo2/default.nix
index eb3a13593480..04ab9a5b5ab3 100644
--- a/pkgs/applications/science/logic/leo2/default.nix
+++ b/pkgs/applications/science/logic/leo2/default.nix
@@ -11,10 +11,10 @@ let
     (builtins.attrNames (builtins.removeAttrs x helperArgNames));
   sourceInfo = rec {
     baseName="leo2";
-    version="1.2.6";
+    version="1.2.8";
     name="${baseName}_v${version}";
     url="http://www.ags.uni-sb.de/~leo/${name}.tgz";
-    hash="0gjgcm6nb9kzdl0y72sgvf2w2q92s1ix70lh6wjz9lj2qdf7gi1z";
+    hash="d46a94f5991623386eb9061cfb0d748e258359a8c690fded173d45303e0e9e3a";
   };
 in
 rec {
diff --git a/pkgs/applications/science/logic/matita/Makefile.patch b/pkgs/applications/science/logic/matita/Makefile.patch
new file mode 100644
index 000000000000..64c9a13f2d07
--- /dev/null
+++ b/pkgs/applications/science/logic/matita/Makefile.patch
@@ -0,0 +1,11 @@
+--- matita-0.5.8/Makefile	2009-12-01 18:21:00.000000000 -0500
++++ matita-0.5.8/Makefile	2010-09-16 10:33:59.665461260 -0400
+@@ -38,7 +38,7 @@
+ uninstall: $(foreach d,$(SUBDIRS),rec@uninstall@$(d))
+ 
+ rec@%:
+-	$(MAKE) -C $(word 2, $(subst @, ,$*)) $(word 1, $(subst @, ,$*)) DESTDIR=$(shell pwd)/$(DESTDIR)
++	$(MAKE) -C $(word 2, $(subst @, ,$*)) $(word 1, $(subst @, ,$*))
+ 
+ # {{{ Distribution stuff
+ 
diff --git a/pkgs/applications/science/logic/matita/configure.patch b/pkgs/applications/science/logic/matita/configure.patch
new file mode 100644
index 000000000000..9a3bbbb13f52
--- /dev/null
+++ b/pkgs/applications/science/logic/matita/configure.patch
@@ -0,0 +1,36 @@
+--- zzz/matita-0.5.8/configure	2009-12-01 18:21:00.000000000 -0500
++++ matita-0.5.8/configure	2010-09-07 19:57:29.732139550 -0400
+@@ -1895,6 +1895,7 @@
+ # look for METAS dir
+ 
+ LIBSPATH="`pwd`/components"
++OLDCAMLPATH="$OCAMLPATH"
+ OCAMLPATH="$LIBSPATH/METAS"
+ 
+ # creating META.*
+@@ -1917,7 +1918,7 @@
+ gdome2 \
+ http \
+ lablgtk2 \
+-lablgtksourceview2.gtksourceview2 \
++lablgtk2.gtksourceview \
+ lablgtkmathview \
+ mysql \
+ netstring \
+@@ -1951,14 +1952,14 @@
+ $FINDLIB_CREQUIRES \
+ lablgtk2.glade \
+ lablgtkmathview \
+-lablgtksourceview2.gtksourceview2 \
++lablgtk2.gtksourceview \
+ helm-xmldiff \
+ "
+ for r in $FINDLIB_LIBSREQUIRES $FINDLIB_REQUIRES
+ do
+   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $r ocaml library" >&5
+ $as_echo_n "checking for $r ocaml library... " >&6; }
+-  if OCAMLPATH=$OCAMLPATH $OCAMLFIND query $r &> /dev/null; then
++  if OCAMLPATH=$OCAMLPATH:$OLDCAMLPATH $OCAMLFIND query $r &> /dev/null; then
+     { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+ $as_echo "yes" >&6; }
+   else
diff --git a/pkgs/applications/science/logic/matita/default.nix b/pkgs/applications/science/logic/matita/default.nix
new file mode 100644
index 000000000000..6ac672193e27
--- /dev/null
+++ b/pkgs/applications/science/logic/matita/default.nix
@@ -0,0 +1,54 @@
+{stdenv, fetchurl, ocaml, camlp5, findlib, gdome2, ocaml_expat, gmetadom, ocaml_http, lablgtk, lablgtkmathview, ocaml_mysql, ocaml_sqlite3, ocamlnet, ulex08, camlzip, ocaml_pcre }:
+
+let
+  ocaml_version = (builtins.parseDrvName ocaml.name).version;
+  version = "0.5.8";
+  pname = "matita";
+
+in
+
+stdenv.mkDerivation {
+  name = "${pname}-${version}";
+
+  src = fetchurl {
+    url = "http://matita.cs.unibo.it/FILES/${pname}-${version}.orig.tar.gz";
+    sha256 = "04sxklfak71khy1f07ks5c6163jbpxv6fmaw03fx8gwwlvpmzglh";
+  };
+
+  buildInputs = [ocaml camlp5 findlib gdome2 ocaml_expat gmetadom ocaml_http lablgtk lablgtkmathview ocaml_mysql ocaml_sqlite3 ocamlnet ulex08 camlzip ocaml_pcre ];
+
+  postPatch = ''
+    BASH=$(type -tp bash)
+    substituteInPlace components/Makefile --replace "SHELL=/bin/bash" "SHELL=$BASH"
+    substituteInPlace matita/Makefile --replace "SHELL=/bin/bash" "SHELL=$BASH"
+    substituteInPlace configure --replace "ulex08" "ulex"
+    substituteInPlace components/METAS/meta.helm-content_pres.src --replace "ulex08" "ulex"
+    substituteInPlace components/content_pres/Makefile --replace "ulex08" "ulex"
+    substituteInPlace components/METAS/meta.helm-grafite_parser.src --replace "ulex08" "ulex"
+    substituteInPlace components/grafite_parser/Makefile --replace "ulex08" "ulex"
+    substituteInPlace configure --replace "zip" "camlzip"
+    substituteInPlace components/METAS/meta.helm-getter.src --replace "zip" "camlzip"
+    substituteInPlace components/METAS/meta.helm-xml.src --replace "zip" "camlzip"
+  '';
+
+  patches = [ ./configure.patch ./Makefile.patch ];
+
+  preConfigure = ''
+    # Setup for findlib.
+    OCAMLPATH=$(pwd)/components/METAS:$OCAMLPATH
+    RTDIR=$out/share/matita
+    export configureFlags="--with-runtime-dir=$RTDIR"
+  '';
+
+  postInstall = ''
+    ensureDir $out/bin
+    ln -vs $RTDIR/matita $RTDIR/matitac $RTDIR/matitaclean $RTDIR/matitadep $RTDIR/matitawiki $out/bin
+  '';
+
+  meta = {
+    homepage = http://matita.cs.unibo.it/;
+    description = "Matita is an experimental, interactive theorem prover";
+    license = "GPLv2+";
+    maintainers = [ stdenv.lib.maintainers.roconnor ];
+  };
+}
diff --git a/pkgs/applications/science/logic/ssreflect/default.nix b/pkgs/applications/science/logic/ssreflect/default.nix
index 61901d545d7a..5a51fe2136a1 100644
--- a/pkgs/applications/science/logic/ssreflect/default.nix
+++ b/pkgs/applications/science/logic/ssreflect/default.nix
@@ -1,13 +1,12 @@
 # TODO:
-# - ssrcoqide does not build successfully (missing coqide libraries in the coq installation).
-# - ssrcoq needs to be invoked with the explicit path to the ssreflect theory
-#   e.g.. ssrcoq -I /nix/store/rp09dlb2y2hpddb0xa7fyrgjlzb284ar-ssreflect-1.2/lib/coq/user-contrib/theories/
+# - coq needs to be invoked with the explicit path to the ssreflect theory
+#   e.g. coqide -R ~/.nix-profile/lib/coq/user-contrib/ ''
 
 {stdenv, fetchurl, ocaml, camlp5, coq}:
 
 let
   pname = "ssreflect";
-  version = "1.2";
+  version = "1.3pl1";
   name = "${pname}-${version}";
   webpage = http://www.msr-inria.inria.fr/Projects/math-components;
 in
@@ -16,18 +15,12 @@ stdenv.mkDerivation {
   inherit name;
 
   src = fetchurl {
-    url = "${webpage}/${name}.tgz";
-    sha256 = "0800b085e6a0caec5093c6c02aacdd8dfd9cc282177e8586f14f9a9e15f64d0b";
+    url = "${webpage}/${name}.tar.gz";
+    sha256 = "0ykrhqb68aanl5d4dmn0vnx8m34gg0jsbdhwx2852rqi7r00b9ri";
   };
 
   buildInputs = [ ocaml camlp5 coq ];
 
-  preBuild = ''
-    coq_makefile -f Make -o Makefile
-    substituteInPlace Makefile \
-      --replace 'install -D $$i $(COQLIB)' 'install -D $$i '$out'/lib/coq'
-  '';
-
   # this fails
   /*
   postBuild = ''
@@ -36,10 +29,9 @@ stdenv.mkDerivation {
   '';
   */
 
-  postInstall = ''
+  installPhase = ''
+    COQLIB=$out/lib/coq make -f Makefile.coq install -e
     ensureDir $out/bin
-    #cp -a bin/ssrcoq bin/ssrcoqide $out/bin
-    cp -a bin/ssrcoq $out/bin
   '';
 
   meta = {
diff --git a/pkgs/applications/science/logic/tptp/default.nix b/pkgs/applications/science/logic/tptp/default.nix
new file mode 100644
index 000000000000..3211b6ebdc01
--- /dev/null
+++ b/pkgs/applications/science/logic/tptp/default.nix
@@ -0,0 +1,87 @@
+x@{builderDefsPackage
+  , yap, tcsh, perl, patchelf, pkgsi686Linux
+  , ...}:
+builderDefsPackage
+(a :  
+let 
+  helperArgNames = ["stdenv" "fetchurl" "builderDefsPackage"] ++ 
+    ["pkgsi686Linux"];
+
+  buildInputs = map (n: builtins.getAttr n x)
+    (builtins.attrNames (builtins.removeAttrs x helperArgNames));
+  sourceInfo = rec {
+    baseName="TPTP";
+    version="5.1.0";
+    name="${baseName}-${version}";
+    url="http://www.cs.miami.edu/~tptp/TPTP/Distribution/TPTP-v${version}.tgz";
+    hash="1wh2k575nn51ykg1jnwfwjqhg5x42k5vvn2spq09px26vhs4yksy";
+  };
+in
+rec {
+  src = a.fetchurl {
+    url = sourceInfo.url;
+    sha256 = sourceInfo.hash;
+  };
+
+  inherit (sourceInfo) name version;
+  inherit buildInputs;
+
+  /* doConfigure should be removed if not needed */
+  phaseNames = ["goTarget" "doUnpack" "fixPlace" "setVars" "installScripts" 
+    "patchBinaries" "makeLinks"];
+
+  goTarget = a.fullDepEntry ''
+    ensureDir "$out"/share/
+    cd "$out"/share/
+  '' ["defEnsureDir" "minInit"];
+
+  fixPlace = a.fullDepEntry ''
+    cd ..
+    mv TPTP-* tptp
+    cd tptp
+  '' ["minInit" "doUnpack"];
+
+  setVars = a.noDepEntry ''
+    export TPTP="$PWD"
+  '';
+
+  installScripts = a.fullDepEntry ''
+    tcsh "$out/share/tptp/Scripts/tptp2T_install" -default
+
+    sed -e 's@^ */bin/@@' -i TPTP2X/*
+
+    tcsh "$out/share/tptp/TPTP2X/tptp2X_install" -default
+  '' ["addInputs"];
+
+  makeLinks = a.fullDepEntry ''
+    ensureDir "$out/bin"
+    ln -s "../share/tptp/TPTP2X/tptp2X" "$out/bin"
+    ln -s "../share/tptp/Scripts/tptp2T" "$out/bin"
+    ln -s "../share/tptp/Scripts/tptp4X" "$out/bin"
+  '' ["defEnsureDir" "minInit"];
+
+  patchBinaries = a.fullDepEntry ''
+    patchelf --set-interpreter "${pkgsi686Linux.glibc}"/lib/ld-linux.so.* \
+      "Scripts/tptp4X"
+  '' ["addInputs"];
+      
+  meta = {
+    description = "Thousands of problems for theorem provers and tools";
+    maintainers = with a.lib.maintainers;
+    [
+      raskin
+    ];
+    # A GiB of data. Installation is unpacking and editing a few files.
+    # No sense in letting Hydra build it.
+    # Also, it is unclear what is covered by "verbatim" - we will edit configs
+    platforms = with a.lib.platforms;
+      [];
+    license = "verbatim-redistribution";
+  };
+  passthru = {
+    updateInfo = {
+      downloadPage = "http://tptp.org/";
+    };
+  };
+}) x
+
diff --git a/pkgs/applications/science/math/ecm/default.nix b/pkgs/applications/science/math/ecm/default.nix
new file mode 100644
index 000000000000..5d378a48dd9e
--- /dev/null
+++ b/pkgs/applications/science/math/ecm/default.nix
@@ -0,0 +1,27 @@
+{stdenv, fetchurl, gmp}:
+
+let
+  pname = "ecm";
+  version = "6.2.3";
+  name = "${pname}-${version}";
+in
+
+stdenv.mkDerivation {
+  inherit name;
+
+  src = fetchurl {
+      url = https://gforge.inria.fr/frs/download.php/22124/ecm-6.2.3.tar.gz;
+      sha256 = "1iwwhbz5vwl7j6dyh292hahc8yy16pq9mmm7mxy49zhxd81vy08p";
+    };
+
+  buildInputs = [ gmp ];
+
+  doCheck = true;
+
+  meta = {
+    description = "Elliptic Curve Method for Integer Factorization";
+    license = stdenv.lib.licenses.gpl2Plus;
+    homepage = http://ecm.gforge.inria.fr/;
+    maintainers = [ stdenv.lib.maintainers.roconnor ];
+  };
+}
diff --git a/pkgs/applications/science/math/eukleides/default.nix b/pkgs/applications/science/math/eukleides/default.nix
new file mode 100644
index 000000000000..9f65bcb8c148
--- /dev/null
+++ b/pkgs/applications/science/math/eukleides/default.nix
@@ -0,0 +1,37 @@
+{ stdenv, fetchurl, bison, flex, texinfo, readline, texLive }:
+
+let
+  name    = "eukleides";
+  version = "1.5.4";
+in
+stdenv.mkDerivation {
+  name = "${name}-${version}";
+
+  src = fetchurl {
+    url = "http://www.eukleides.org/files/${name}-${version}.tar.bz2";
+    sha256 = "0s8cyh75hdj89v6kpm3z24i48yzpkr8qf0cwxbs9ijxj1i38ki0q";
+  };
+
+  buildInputs = [bison flex texinfo readline texLive];
+
+  preConfigure = "sed -i 's/ginstall-info/install-info/g' doc/Makefile";
+  installPhase = "ensureDir $out/bin ; make PREFIX=$out install";
+
+  meta = {
+    description = "Geometry Drawing Language";
+    homepage = "http://www.eukleides.org/";
+    license = "GPLv2";
+
+    longDescription = ''
+      Eukleides is a computer language devoted to elementary plane
+      geometry. It aims to be a fairly comprehensive system to create
+      geometric figures, either static or dynamic. Eukleides allows to
+      handle basic types of data: numbers and strings, as well as
+      geometric types of data: points, vectors, sets (of points), lines,
+      circles and conics.
+    '';
+
+    platforms = stdenv.lib.platforms.all;
+    maintainers = [ stdenv.lib.maintainers.simons ];
+  };
+}
diff --git a/pkgs/applications/science/math/jags/default.nix b/pkgs/applications/science/math/jags/default.nix
new file mode 100644
index 000000000000..3043df15da74
--- /dev/null
+++ b/pkgs/applications/science/math/jags/default.nix
@@ -0,0 +1,17 @@
+{stdenv, fetchurl, gfortran, liblapack, blas}:
+
+stdenv.mkDerivation rec {
+  name = "JAGS-2.2.0";
+  src = fetchurl {
+    url = "mirror://sourceforge/mcmc-jags/${name}.tar.gz";
+    sha256 = "016xml4k99lmdwwjiabxin95k9p3q2zh4pcci8wwcqwlq5y205b6";
+  };
+  buildInputs = [gfortran liblapack blas];
+
+  meta = {
+    description = "JAGS: Just Another Gibbs Sampler";
+    license     = "GPL2";
+    homepage    = http://www-ice.iarc.fr/~martyn/software/jags/;
+    maintainers = [stdenv.lib.maintainers.andres];
+  };
+}
diff --git a/pkgs/applications/science/math/maxima/default.nix b/pkgs/applications/science/math/maxima/default.nix
index f99c1e46162e..f8f21d8909b4 100644
--- a/pkgs/applications/science/math/maxima/default.nix
+++ b/pkgs/applications/science/math/maxima/default.nix
@@ -1,22 +1,40 @@
-{ stdenv, fetchurl, clisp }:
+{ stdenv, fetchurl, sbcl, texinfo, perl, makeWrapper, rlwrap ? null, tk ? null, gnuplot ? null }:
 
 let
-    name    = "maxima";
-    version = "5.22.1";
+  name    = "maxima";
+  version = "5.25.0";
+
+  searchPath =
+    stdenv.lib.makeSearchPath "bin"
+      (stdenv.lib.filter (x: x != null) [ sbcl rlwrap tk gnuplot ]);
 in
 stdenv.mkDerivation {
   name = "${name}-${version}";
 
   src = fetchurl {
     url = "mirror://sourceforge/${name}/${name}-${version}.tar.gz";
-    sha256 = "0sdrv3lra6j3ylaqsblnd3x7rq4ybafyj7rb114ycadpx2qf06lq";
+    sha256 = "49c90fb809f5027787600050503476193db3620fd9517f620b82ad492ba30c0a";
   };
 
-  preConfigure = ''
-    configureFlags="--infodir=$out/share/info --mandir=$out/share/man"
+  buildInputs = [sbcl texinfo perl makeWrapper];
+
+  postInstall = ''
+    # Make sure that maxima can find its runtime dependencies.
+    for prog in "$out/bin/"*; do
+      wrapProgram "$prog" --prefix PATH ":" "${searchPath}"
+    done
+    # Move emacs modules and documentation into the right place.
+    ensureDir $out/share/emacs $out/share/doc
+    ln -s ../maxima/${version}/emacs $out/share/emacs/site-lisp
+    ln -s ../maxima/${version}/doc $out/share/doc/maxima
   '';
 
-  buildInputs = [clisp];
+  # The regression test suite has minor failures, but curiously enough
+  # this doesn't seem to abort the build process:
+  # <http://sourceforge.net/tracker/?func=detail&aid=3365831&group_id=4933&atid=104933>.
+  doCheck = true;
+
+  enableParallelBuilding = true;
 
   meta = {
     description = "Maxima computer algebra system";
diff --git a/pkgs/applications/science/math/msieve/default.nix b/pkgs/applications/science/math/msieve/default.nix
new file mode 100644
index 000000000000..baee2f23d4ca
--- /dev/null
+++ b/pkgs/applications/science/math/msieve/default.nix
@@ -0,0 +1,28 @@
+{stdenv, fetchurl, zlib, gmp, ecm }:
+
+stdenv.mkDerivation {
+  name = "msieve-1.48";
+
+  src = fetchurl {
+      url = mirror://sourceforge/msieve/msieve/Msieve%20v1.48/msieve148.tar.gz;
+      sha256 = "05cm23mpfsbwssqda243sbi8m31j783qx89x9gl7sy8a4dnv7h63";
+    };
+
+  buildInputs = [ zlib gmp ecm ];
+
+  ECM = if ecm == null then "0" else "1";
+
+  buildFlags = if stdenv.system == "x86_64-linux" then "x86_64"
+               else if stdenv.system == "i686-linux" then "x86"
+               else "generic";
+
+  installPhase = ''ensureDir $out/bin/
+                   cp msieve $out/bin/'';
+
+  meta = {
+    description = "a C library implementing a suite of algorithms to factor large integers";
+    license = stdenv.lib.licenses.publicDomain;
+    homepage = http://msieve.sourceforge.net/;
+    maintainers = [ stdenv.lib.maintainers.roconnor ];
+  };
+}
diff --git a/pkgs/applications/science/math/pari/default.nix b/pkgs/applications/science/math/pari/default.nix
index 62763ac2198a..43291d792b72 100644
--- a/pkgs/applications/science/math/pari/default.nix
+++ b/pkgs/applications/science/math/pari/default.nix
@@ -11,10 +11,10 @@ let
     (builtins.attrNames (builtins.removeAttrs x helperArgNames));
   sourceInfo = rec {
     baseName="pari";
-    version="2.3.5";
+    version="2.5.0";
     name="${baseName}-${version}";
     url="http://pari.math.u-bordeaux.fr/pub/pari/unix/${name}.tar.gz";
-    hash="124xr2jdz2c15v45i1zvgylng44lhf23729a1mk7ci1vywdaxpa7";
+    hash="18ipxj4hzj7s3fqz878fiypkzrkbjj8wvbygz9j8c3ya06q27jax";
   };
 in
 rec {
diff --git a/pkgs/applications/science/math/wxmaxima/default.nix b/pkgs/applications/science/math/wxmaxima/default.nix
index ece6eb985178..6bd6e9266e6b 100644
--- a/pkgs/applications/science/math/wxmaxima/default.nix
+++ b/pkgs/applications/science/math/wxmaxima/default.nix
@@ -1,22 +1,29 @@
-{ stdenv, fetchurl, maxima, wxGTK }:
-
-# TODO: Build the correct ${maxima}/bin/maxima store path into wxMaxima so that
-#       it can run that binary without relying on $PATH, /etc/wxMaxima.conf, or
-#       ~/.wxMaxima.
+{ stdenv, fetchurl, maxima, wxGTK, makeWrapper }:
 
 let
-    name    = "wxmaxima";
-    version = "0.8.6";
+  name    = "wxmaxima";
+  version = "11.04.0";
 in
 stdenv.mkDerivation {
   name = "${name}-${version}";
 
   src = fetchurl {
     url = "mirror://sourceforge/${name}/wxMaxima-${version}.tar.gz";
-    sha256 = "09w6gai0jfhl959yrdcdikz5l9kdjshasjk404vl19nfnivdbj9f";
+    sha256 = "1dfwh5ka125wr6wxzyiwz16lk8kaf09rb6lldzryjwh8zi7yw8dm";
   };
 
-  buildInputs = [maxima wxGTK];
+  buildInputs = [wxGTK maxima makeWrapper];
+
+  postInstall = ''
+    # Make sure that wxmaxima can find its runtime dependencies.
+    for prog in "$out/bin/"*; do
+      wrapProgram "$prog" --prefix PATH ":" "${maxima}/bin"
+    done
+  '';
+
+  doCheck = true;
+
+  enableParallelBuilding = true;
 
   meta = {
     description = "Cross platform GUI for the computer algebra system Maxima.";
diff --git a/pkgs/applications/science/misc/tulip/configure-opengl.patch b/pkgs/applications/science/misc/tulip/configure-opengl.patch
deleted file mode 100644
index e5346ef07283..000000000000
--- a/pkgs/applications/science/misc/tulip/configure-opengl.patch
+++ /dev/null
@@ -1,75 +0,0 @@
-Remove broken detection of OpenGL and GLEW.  See
-<http://sourceforge.net/tracker/?func=detail&aid=3015936&group_id=61223&atid=496518>.
-
---- tulip-3.3.1/acinclude.m4	2010-01-18 20:34:02.000000000 +0100
-+++ tulip-3.3.1/acinclude.m4	2010-06-14 16:25:25.000000000 +0200
-@@ -353,68 +353,8 @@ AC_ARG_WITH(gl-libraries,
-     [  ac_gl_libraries="$withval"
-     ])
- 
--AC_CACHE_VAL(ac_cv_have_gl,
--[
--if test ${VAR_WIN32} = 1
--then
--gl_incdirs=" /mingw/include $ac_gl_includes $GLDIR/include /usr/include /usr/X11R6/include/X11 /usr/X11R6/include $x_includes "
--else
--gl_incdirs=" $ac_gl_includes $GLDIR/include /usr/include /usr/X11R6/include/X11 /usr/X11R6/include $x_includes "
--fi
--AC_FIND_FILE(GL/gl.h, $gl_incdirs, gl_incdir)
--ac_gl_includes="$gl_incdir"
--
--if test ${VAR_WIN32} = 1
--then
--gl_libdirs="$GLDIR $ac_gl_libraries $GLLIB /usr/X11R6/lib /usr/lib /usr/local/lib $x_libraries "
--else
--gl_libdirs="$ac_gl_libraries $GLLIB /usr/X11R6/lib64 /usr/lib64 /usr/local/lib64/usr/X11R6/lib /usr/lib /usr/local/lib $x_libraries "
--fi
--
--test -n "$GLDIR" && gl_libdirs="$GLDIR/lib64 $GLDIR/lib $GLDIR $gl_libdirs"
--test=NONE
--gl_libdir=NONE
--for dir in $gl_libdirs; do
--if test ${VAR_WIN32} = 1
--then
--  try="ls -1 $dir/*opengl*"
--else
--  try="ls -1 $dir/libGL*"
--fi
--  if test=`eval $try 2> /dev/null`; then 
--    gl_libdir=$dir
--    if test ${VAR_WIN32} = 0 ; then 	 
--      try="ls -1 $gl_libdir/libGLEW.*" 	 
--      if test=`eval $try 2> /dev/null`; then break; else AC_MSG_ERROR([ libGLEW not found , please install it in $gl_libdir ]); fi 	 
--    else 	 
--      break 	 
--    fi
--  else 
--    echo "tried $dir" >&AC_FD_CC
--  fi
--done
--ac_gl_libraries="$gl_libdir"
- ])
- 
--eval "$ac_cv_have_gl"
--if test "$ac_gl_libraries" = NONE; then
--  AC_MSG_ERROR([ Not found , put your GLDIR environnement variable to the OpenGL directory ]);
--else
--  ac_cv_have_gl="have_gl=yes \
--  ac_gl_includes=$ac_gl_includes ac_gl_libraries=$ac_gl_libraries"
--  AC_MSG_RESULT([ libraries $ac_gl_libraries, headers $ac_gl_includes ])  
--  gl_libraries="$ac_gl_libraries"
--  gl_includes="$ac_gl_includes"
--if test ${VAR_MACOSX} = 1
--then
--  GL_INCLUDES="-I$ac_gl_includes"
--  GL_LDFLAGS=""
--else
--  GL_INCLUDES="-I$ac_gl_includes"	
--  GL_LDFLAGS="-L$ac_gl_libraries"
--fi
--fi
--
- dnl MAC PORT
- if test ${VAR_MACOSX} = 1
- then
-
diff --git a/pkgs/applications/science/misc/tulip/default.nix b/pkgs/applications/science/misc/tulip/default.nix
index 3bca42023e9f..b213c14cc1a5 100644
--- a/pkgs/applications/science/misc/tulip/default.nix
+++ b/pkgs/applications/science/misc/tulip/default.nix
@@ -1,31 +1,23 @@
 { fetchurl, stdenv, libxml2, freetype, mesa, glew, qt
-, autoconf, automake, libtool }:
+, autoconf, automake, libtool, cmake, makeWrapper }:
 
-let version = "3.4.0"; in
+let version = "3.5.0"; in
 stdenv.mkDerivation rec {
   name = "tulip-${version}";
 
   src = fetchurl {
-    url = "mirror://sourceforge/auber/tulip/tulip-${version}/${name}.tar.bz2";
-    sha256 = "2889113f773ba539472d501fb4f45dbf5eb76e02c949dfa74c63f6f815a2baab";
+    url = "mirror://sourceforge/auber/tulip/tulip-${version}/${name}-src.tar.gz";
+    sha256 = "0wl0wqjlifpay61pn7dxr3dl5r4a7v80f5g277p6s06ibvn2p3ln";
   };
 
-  patches = [ ./configure-opengl.patch ];
-
-  preConfigure =
-    '' export CPATH="${mesa}/include:${glew}/include"
-       export LIBRARY_PATH="${mesa}/lib:${glew}/lib"
-       export QTDIR="${qt}"
-       export LDFLAGS="-lGLEW"
-
-       rm -vf aclocal.m4 ltmain.sh
-       autoreconf -fi
-    '';
-
   buildInputs = [ libxml2 freetype glew ]
-    ++ [ autoconf automake libtool ];
+    ++ [ autoconf automake libtool cmake qt makeWrapper ];
   propagagedBuildInputs = [ mesa qt ];
 
+  postInstall=''
+    wrapProgram "$out/bin/tulip"
+  '';
+
   # FIXME: "make check" needs Docbook's DTD 4.4, among other things.
   doCheck = false;