11 files changed, 177 insertions, 26 deletions
diff --git a/pkgs/applications/science/misc/boinc/default.nix b/pkgs/applications/science/misc/boinc/default.nix
index 0bc5c3cb7c7c..7020de0bca88 100644
--- a/pkgs/applications/science/misc/boinc/default.nix
+++ b/pkgs/applications/science/misc/boinc/default.nix
@@ -3,12 +3,12 @@ mesa, libXmu, libXi, freeglut, libjpeg, libtool, wxGTK, xcbutil,
 sqlite, gtk, patchelf, libXScrnSaver, libnotify, libX11, libxcb }:
 
 stdenv.mkDerivation rec {
-  name = "boinc-7.0.44";
+  name = "boinc-7.2.42";
 
   src = fetchgit {
     url = "git://boinc.berkeley.edu/boinc-v2.git";
-    rev = "7c449b1fb8a681ceb27d6895751b62a2b3adf0f2";
-    sha256 = "0hdramyl9nip3gadp7xiaz8ngyld15i93d8ai1nsd04bmrvdfqia";
+    rev = "dd0d630882547c123ca0f8fda7a62e058d60f6a9";
+    sha256 = "1zifpi3mjgaj68fba6kammp3x7z8n2x164zz6fj91xfiapnan56j";
   };
 
   buildInputs = [ libtool automake autoconf m4 pkgconfig curl mesa libXmu libXi
@@ -36,7 +36,7 @@ stdenv.mkDerivation rec {
 
     homepage = http://boinc.berkeley.edu/;
 
-    license = "LGPLv2+";
+    license = stdenv.lib.licenses.lgpl2Plus;
 
     platforms = stdenv.lib.platforms.linux;  # arbitrary choice
   };
diff --git a/pkgs/applications/science/misc/fityk/default.nix b/pkgs/applications/science/misc/fityk/default.nix
new file mode 100644
index 000000000000..db79839ba669
--- /dev/null
+++ b/pkgs/applications/science/misc/fityk/default.nix
@@ -0,0 +1,23 @@
+{ stdenv, fetchurl, wxGTK30, boost, lua, zlib, bzip2, xylib, readline, gnuplot }:
+
+let
+  name    = "fityk";
+  version = "1.2.9";
+in
+stdenv.mkDerivation {
+  name = "${name}-${version}";
+
+  src = fetchurl {
+    url = "https://github.com/wojdyr/fityk/releases/download/v${version}/${name}-${version}.tar.bz2";
+    sha256 = "1gl938nd2jyya8b3gzbagm1jab2mkc9zvr6zsg5d0vkfdqlk0pv1";
+  };
+
+  buildInputs = [wxGTK30 boost lua zlib bzip2 xylib readline gnuplot ];
+
+  meta = {
+    description = "Fityk -- curve fitting and peak fitting software";
+    license = "GPL2";
+    homepage = http://fityk.nieto.pl/;
+    platforms = stdenv.lib.platforms.linux;
+  };
+}
diff --git a/pkgs/applications/science/misc/golly/default.nix b/pkgs/applications/science/misc/golly/default.nix
index a380f05b0915..9d198cd5c7f8 100644
--- a/pkgs/applications/science/misc/golly/default.nix
+++ b/pkgs/applications/science/misc/golly/default.nix
@@ -1,11 +1,11 @@
-x@{builderDefsPackage, 
+x@{builderDefsPackage,
   wxGTK, perl, python, zlib
   , ...}:
 builderDefsPackage
-(a :  
-let 
+(a :
+let
   s = import ./src-for-default.nix;
-  helperArgNames = ["builderDefsPackage"] ++ 
+  helperArgNames = ["builderDefsPackage"] ++
     [];
   buildInputs = map (n: builtins.getAttr n x)
     (builtins.attrNames (builtins.removeAttrs x helperArgNames));
@@ -26,7 +26,7 @@ rec {
     export NIX_LDFLAGS="$NIX_LDFLAGS -l$pythonLib"
     echo "Flags: $NIX_LDFLAGS"
   '';
-      
+
   meta = {
     description = "Cellular automata simulation program";
     maintainers = with a.lib.maintainers;
@@ -35,7 +35,7 @@ rec {
     ];
     platforms = with a.lib.platforms;
       linux;
-    license = "GPLv2";
+    license = with a.lib.licenses;
+      gpl2;
   };
 }) x
-
diff --git a/pkgs/applications/science/misc/megam/default.nix b/pkgs/applications/science/misc/megam/default.nix
new file mode 100644
index 000000000000..a0ee505dc97f
--- /dev/null
+++ b/pkgs/applications/science/misc/megam/default.nix
@@ -0,0 +1,46 @@
+{ fetchurl, stdenv, ocaml, makeWrapper, ncurses }:
+
+let version = "0.92"; in
+stdenv.mkDerivation rec {
+  name = "megam-${version}";
+
+  src = fetchurl {
+    url = "http://hal3.name/megam/megam_src.tgz";
+    sha256 = "dc0e9f59ff8513449fe3bd40b260141f89c88a4edf6ddc8b8a394c758e49724e";
+  };
+
+  patches = [ ./ocaml-includes.patch ./ocaml-3.12.patch ];
+  
+  buildInputs = [ ocaml ncurses ];
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  makeFlags = "CAML_INCLUDES=${ocaml}/lib/ocaml/caml";
+
+  # see https://bugzilla.redhat.com/show_bug.cgi?id=435559
+  dontStrip = true;
+
+  installPhase = ''
+    mkdir -pv $out/bin
+    cp -Rv megam $out/bin
+  '';
+
+
+  meta = {
+    description = "MEGA Model Optimization Package";
+
+    longDescription =
+      ''  The software here is an implementation of maximum likelihood
+          and maximum a posterior optimization of the parameters of
+          these models.  The algorithms used are much more efficient
+          than the iterative scaling techniques used in almost every
+          other maxent package out there.  '';
+
+    homepage = http://www.umiacs.umd.edu/~hal/megam;
+
+    license = "non-commercial";
+
+    maintainers = [ ];
+    platforms = stdenv.lib.platforms.gnu;  # arbitrary choice
+  };
+}
diff --git a/pkgs/applications/science/misc/megam/ocaml-3.12.patch b/pkgs/applications/science/misc/megam/ocaml-3.12.patch
new file mode 100644
index 000000000000..8265acf6e4a7
--- /dev/null
+++ b/pkgs/applications/science/misc/megam/ocaml-3.12.patch
@@ -0,0 +1,12 @@
+diff -ru megam_0.92/Makefile megam_0.92-b/Makefile
+--- megam_0.92/Makefile	2007-10-08 18:06:04.000000000 +0100
++++ megam_0.92-b/Makefile	2013-11-25 10:14:20.000000000 +0000
+@@ -59,7 +59,7 @@
+ 
+ WITHUNIX =unix.cma -cclib -lunix
+ 
+-WITHSTR =str.cma -cclib -lstr
++WITHSTR =str.cma -cclib -lcamlstr
+ 
+ WITHBIGARRAY =bigarray.cma -cclib -lbigarray
+ 
diff --git a/pkgs/applications/science/misc/megam/ocaml-includes.patch b/pkgs/applications/science/misc/megam/ocaml-includes.patch
new file mode 100644
index 000000000000..b3a56643448c
--- /dev/null
+++ b/pkgs/applications/science/misc/megam/ocaml-includes.patch
@@ -0,0 +1,21 @@
+diff -ru megam_0.92/Makefile megam_0.92-b/Makefile
+--- megam_0.92/Makefile	2007-10-08 18:06:04.000000000 +0100
++++ megam_0.92-b/Makefile	2013-11-25 10:14:20.000000000 +0000
+@@ -41,7 +41,7 @@
+ #
+ # The Caml compilers. #
+ # You may fix here the path to access the Caml compiler on your machine
+-CAMLC = ocamlc -g
++CAMLC = ocamlc -g $(WITHCLIBS)
+ CAMLOPT = ocamlopt -unsafe -ccopt -O4 -ccopt -ffast-math -inline 99999 
+ CAMLDEP = ocamldep
+ CAMLLEX = ocamllex
+@@ -70,7 +70,7 @@
+ WITHDBM =dbm.cma -cclib -lmldbm -cclib -lndbm
+ 
+ #WITHCLIBS =-I /usr/lib/ocaml/3.09.2/caml
+-WITHCLIBS =-I /usr/lib/ocaml/caml
++WITHCLIBS =-I $(CAML_INCLUDES) 
+ 
+ ################ End of user's variables #####################
+ 
diff --git a/pkgs/applications/science/misc/root/cmake.patch b/pkgs/applications/science/misc/root/cmake.patch
new file mode 100644
index 000000000000..b6efd7444fe9
--- /dev/null
+++ b/pkgs/applications/science/misc/root/cmake.patch
@@ -0,0 +1,11 @@
+--- cmake/modules/RootBuildOptions.cmake	1969-12-31 20:30:01.000000000 -0330
++++ cmake/modules/RootBuildOptions.cmake	2014-01-10 14:09:29.424937408 -0330
+@@ -149,7 +149,7 @@
+ 
+ #---General Build options----------------------------------------------------------------------
+ # use, i.e. don't skip the full RPATH for the build tree
+-set(CMAKE_SKIP_BUILD_RPATH  FALSE)
++set(CMAKE_SKIP_BUILD_RPATH  TRUE)
+ # when building, don't use the install RPATH already (but later on when installing)
+ set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) 
+ # add the automatically determined parts of the RPATH
diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix
new file mode 100644
index 000000000000..1227e76ac0c5
--- /dev/null
+++ b/pkgs/applications/science/misc/root/default.nix
@@ -0,0 +1,27 @@
+{ stdenv, fetchurl, cmake, mesa, libX11, gfortran, libXpm, libXft, libXext, zlib }:
+
+stdenv.mkDerivation rec {
+  name = "root-${version}";
+  version = "5.34.15";
+
+  src = fetchurl {
+    url = "ftp://root.cern.ch/root/root_v${version}.source.tar.gz";
+    sha256 = "1bkiggcyya39a794d3d2rzzmmkbdymf86hbqhh0l1pl4f38xvp6i";
+  };
+
+  buildInputs = [ cmake gfortran mesa libX11 libXpm libXft libXext zlib ];
+
+  # CMAKE_INSTALL_RPATH_USE_LINK_PATH is set to FALSE in
+  # <rootsrc>/cmake/modules/RootBuildOptions.cmake.
+  # This patch sets it to TRUE.
+  patches = [ ./cmake.patch ];
+  patchFlags = "-p0";
+
+  enableParallelBuilding = true;
+
+  meta = {
+    homepage = "http://root.cern.ch/drupal/";
+    description = "A data analysis framework";
+    platforms = stdenv.lib.platforms.linux;
+  };
+}
diff --git a/pkgs/applications/science/misc/simgrid/default.nix b/pkgs/applications/science/misc/simgrid/default.nix
index 5fdede1abcdf..29a7caf769be 100644
--- a/pkgs/applications/science/misc/simgrid/default.nix
+++ b/pkgs/applications/science/misc/simgrid/default.nix
@@ -1,20 +1,19 @@
-{ fetchurl, stdenv, cmake, perl, ruby }:
+{ fetchurl, stdenv, cmake, perl, ruby, boost, lua5_1, graphviz, libsigcxx
+, libunwind, elfutils
+}:
 
 stdenv.mkDerivation rec {
-  name = "simgrid-3.5";
+  version = "3.11.1";
+  name = "simgrid-${version}";
 
   src = fetchurl {
-    url = "https://gforge.inria.fr/frs/download.php/28017/${name}.tar.gz";
-    sha256 = "1vd4pvrcyii1nfwyca3kpbwshbc965lfpn083zd8rigg6ydchq8y";
+    url = "https://gforge.inria.fr/frs/download.php/33686/${name}.tar.gz";
+    sha256 = "0mkrzxpf42lmn96khfl1791vram67r2nqsgmppd2yil889nyz5kp";
   };
 
-  /* FIXME: Ruby currently disabled because of this:
-
-     Linking C shared library ../src/.libs/libsimgrid.so
-     ld: cannot find -lruby-1.8.7-p72
-
-   */
-  buildInputs = [ cmake perl /* ruby */ ];
+  buildInputs = [ cmake perl ruby boost lua5_1 graphviz libsigcxx libunwind
+    elfutils
+    ];
 
   preConfigure =
     # Make it so that libsimgrid.so will be found when running programs from
@@ -22,8 +21,17 @@ stdenv.mkDerivation rec {
     '' export LD_LIBRARY_PATH="$PWD/src/.libs"
        export cmakeFlags="-Dprefix=$out"
 
-       # Enable tracing.
-       export cmakeFlags="$cmakeFlags -Denable_tracing=on"
+       export NIX_CFLAGS_COMPILE="$NIX_CFLAGS_COMPILE
+         -isystem $(echo "${libsigcxx}/lib/"sigc++*/include)
+	 -isystem $(echo "${libsigcxx}/include"/sigc++* )
+	 "
+       export CMAKE_PREFIX_PATH="$CMAKE_PREFIX_PATH:$(echo "${libsigcxx}/lib/"sigc++*)"
+
+       # Enable more functionality.
+       export cmakeFlags="$cmakeFlags -Denable_tracing=on -Denable_jedule=on
+         -Denable_latency_bound_tracking=on -Denable_lua=on
+	 -Denable_ns3=on -Denable_gtnets=on
+	 "
     '';
 
   makeFlags = "VERBOSE=1";
@@ -45,6 +53,7 @@ stdenv.mkDerivation rec {
   patchPhase =
     '' for i in "src/smpi/"*
        do
+         test -f "$i" &&
          sed -i "$i" -e's|/bin/bash|/bin/sh|g'
        done
 
@@ -71,7 +80,7 @@ stdenv.mkDerivation rec {
 
     homepage = http://simgrid.gforge.inria.fr/;
 
-    license = "LGPLv2+";
+    license = stdenv.lib.licenses.lgpl2Plus;
 
     maintainers = [ ];
     platforms = stdenv.lib.platforms.gnu;  # arbitrary choice
diff --git a/pkgs/applications/science/misc/tulip/default.nix b/pkgs/applications/science/misc/tulip/default.nix
index e58183a4f40b..da6e0cb2805d 100644
--- a/pkgs/applications/science/misc/tulip/default.nix
+++ b/pkgs/applications/science/misc/tulip/default.nix
@@ -30,7 +30,7 @@ stdenv.mkDerivation rec {
 
     homepage = http://tulip.labri.fr/;
 
-    license = "GPLv3+";
+    license = stdenv.lib.licenses.gpl3Plus;
 
     maintainers = [ ];
     platforms = stdenv.lib.platforms.gnu;  # arbitrary choice
diff --git a/pkgs/applications/science/misc/vite/default.nix b/pkgs/applications/science/misc/vite/default.nix
index 4c1cf318b5a2..2e25ff582ee9 100644
--- a/pkgs/applications/science/misc/vite/default.nix
+++ b/pkgs/applications/science/misc/vite/default.nix
@@ -44,5 +44,7 @@ stdenv.mkDerivation {
 
     maintainers = [ stdenv.lib.maintainers.ludo ];
     platforms = stdenv.lib.platforms.gnu;  # arbitrary choice
+
+    broken = true;
   };
 }