Add 'nixpkgs/' from commit 'abf060725d7614bd3b9f96764262dfbc2f9c2199'

git-subtree-dir: nixpkgs
git-subtree-mainline: 4e31070265257dc67d120c27e0f75c2344fdfa9a
git-subtree-split: abf060725d7614bd3b9f96764262dfbc2f9c2199

4 files changed, 216 insertions, 0 deletions

diff --git a/nixpkgs/pkgs/applications/science/programming/fdr/default.nix b/nixpkgs/pkgs/applications/science/programming/fdr/default.nix
new file mode 100644
index 000000000000..3bfb70f5ce8e
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/programming/fdr/default.nix
@@ -0,0 +1,69 @@
+{stdenv, fetchurl, qtbase, qtx11extras, ncurses, xorg, zlib, python27Packages}:
+stdenv.mkDerivation {
+  name = "fdr-4.2.3";
+  src = fetchurl {
+    url = https://www.cs.ox.ac.uk/projects/fdr/downloads/fdr-3789-linux-x86_64.tar.gz;
+    sha256 = "0n2yqichym5xdawlgk3r7yha88k7ycnx6585jfrcm7043sls1i88";
+  };
+
+  libPath = stdenv.lib.makeLibraryPath [
+    stdenv.cc.cc
+    python27Packages.python
+    qtbase
+    qtx11extras
+    ncurses
+    xorg.libX11
+    xorg.libXft
+    zlib
+  ];
+
+  phases = [ "unpackPhase" "installPhase" ];
+  installPhase = ''
+    mkdir -p "$out"
+
+    # shipped Qt is buggy
+    rm lib/libQt*
+    rm -r lib/qt_plugins
+
+    cp -r * "$out"
+    # Hack around lack of libtinfo in NixOS
+    ln -s ${ncurses.out}/lib/libncursesw.so.6 $out/lib/libtinfo.so.5
+    ln -s ${qtbase.bin}/${qtbase.qtPluginPrefix} $out/lib/qt_plugins
+    ln -s ${zlib.out}/lib/libz.so.1 $out/lib/libz.so.1
+
+    for b in fdr4 _fdr4 refines _refines cspmprofiler cspmexplorerprof
+    do
+      patchelf --set-interpreter $(cat $NIX_CC/nix-support/dynamic-linker) \
+        --set-rpath "$libPath:$out/lib" \
+        "$out/bin/$b"
+    done
+
+    for l in corei7/librefines.so \
+      libcspm_process_compiler.so \
+      libcsp_operators.so \
+      _fdr.so \
+      libfdr.so \
+      libfdr_java.so \
+      libprocess_compiler.so \
+      librefines_gui.so \
+      librefines_licensing.so  \
+      libboost_date_time.so.1.60.0 \
+      libboost_filesystem.so.1.60.0 \
+      libboost_iostreams.so.1.60.0 \
+      libboost_program_options.so.1.60.0 \
+      libboost_serialization.so.1.60.0 \
+      libboost_system.so.1.60.0
+    do
+      patchelf --set-rpath "$libPath:$out/lib" \
+        "$out/lib/$l"
+    done
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://www.cs.ox.ac.uk/projects/fdr/;
+    description = "The CSP refinement checker";
+    license = licenses.unfreeRedistributable;
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ nickhu ];
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/programming/plm/default.nix b/nixpkgs/pkgs/applications/science/programming/plm/default.nix
new file mode 100644
index 000000000000..c454ad377686
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/programming/plm/default.nix
@@ -0,0 +1,36 @@
+{stdenv, fetchurl, makeWrapper, jre, gcc, valgrind}:
+# gcc and valgrind are not strict dependencies, they could be made
+# optional. They are here because plm can only help you learn C if you
+# have them installed.
+stdenv.mkDerivation rec {
+  major = "2";
+  minor = "5";
+  version = "${major}-${minor}";
+  name = "plm-${version}";
+
+  src = fetchurl {
+    url = "http://webloria.loria.fr/~quinson/Teaching/PLM/plm-${major}_${minor}.jar";
+    sha256 = "0m17cxa3nxi2cbswqvlfzp0mlfi3wrkw8ry2xhkxy6aqzm2mlgcc";
+    name = "${name}.jar";
+  };
+
+  buildInputs = [ makeWrapper jre gcc valgrind ];
+
+  phases = [ "installPhase" ];
+
+  installPhase = ''
+    mkdir -p "$prefix/bin"
+
+    makeWrapper ${jre}/bin/java $out/bin/plm \
+      --add-flags "-jar $src" \
+      --prefix PATH : "$PATH"
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Free cross-platform programming exerciser";
+    license = licenses.gpl3;
+    maintainers = [ ];
+    platforms = stdenv.lib.platforms.all;
+    broken = true;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/programming/scyther/cli.nix b/nixpkgs/pkgs/applications/science/programming/scyther/cli.nix
new file mode 100644
index 000000000000..152b71217743
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/programming/scyther/cli.nix
@@ -0,0 +1,32 @@
+{ stdenv, glibc, flex, bison, cmake
+, version, src, meta }:
+stdenv.mkDerivation {
+  name = "scyther-cli-${version}";
+
+  inherit src meta;
+
+  buildInputs = [
+    cmake
+    glibc.static
+    flex
+    bison
+  ];
+
+  patchPhase = ''
+    # Since we're not in a git dir, the normal command this project uses to create this file wouldn't work
+    printf "%s\n" "#define TAGVERSION \"${version}\"" > src/version.h
+  '';
+
+  configurePhase = ''
+    (cd src && cmakeConfigurePhase)
+  '';
+
+  dontUseCmakeBuildDir = true;
+  cmakeFlags = [ "-DCMAKE_C_FLAGS=-std=gnu89" ];
+
+  installPhase = ''
+    mkdir -p "$out/bin"
+    mv src/scyther-linux "$out/bin/scyther-cli"
+    ln -s "$out/bin/scyther-cli" "$out/bin/scyther-linux"
+  '';
+}
diff --git a/nixpkgs/pkgs/applications/science/programming/scyther/default.nix b/nixpkgs/pkgs/applications/science/programming/scyther/default.nix
new file mode 100644
index 000000000000..e0993a580193
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/programming/scyther/default.nix
@@ -0,0 +1,79 @@
+{ stdenv, lib, buildEnv, pkgsi686Linux, fetchFromGitHub, python27Packages, graphviz
+, includeGUI ? true
+, includeProtocols ? true
+}:
+let
+  version = "1.1.3";
+
+  src = fetchFromGitHub {
+    rev = "v${version}";
+    sha256 = "0rb4ha5bnjxnwj4f3hciq7kyj96fhw14hqbwl5kr9cdw8q62mx0h";
+    owner = "cascremers";
+    repo = "scyther";
+  };
+
+  meta = with lib; {
+    description = "Scyther is a tool for the automatic verification of security protocols.";
+    homepage = https://www.cs.ox.ac.uk/people/cas.cremers/scyther/;
+    license = licenses.gpl2;
+    maintainers = with maintainers; [ infinisil ];
+    platforms = platforms.linux;
+  };
+
+  cli = pkgsi686Linux.callPackage ./cli.nix {
+    inherit version src meta;
+  };
+
+  gui = stdenv.mkDerivation {
+    name = "scyther-gui-${version}";
+    inherit src meta;
+    buildInputs = [
+      python27Packages.wrapPython
+    ];
+
+    patchPhase = ''
+      file=gui/Scyther/Scyther.py
+
+      # By default the scyther binary is looked for in the directory of the python script ($out/gui), but we want to have it look where our cli package is
+      substituteInPlace $file --replace "return getMyDir()" "return \"${cli}/bin\""
+
+      # Removes the Shebang from the file, as this would be wrapped wrongly
+      sed -i -e "1d" $file
+    '';
+
+    dontBuild = true;
+
+    propagatedBuildInputs = [
+      python27Packages.wxPython
+      graphviz
+    ];
+
+    installPhase = ''
+      mkdir -p "$out"/gui "$out"/bin
+      cp -r gui/* "$out"/gui
+      ln -s "$out"/gui/scyther-gui.py "$out/bin/scyther-gui"
+    '';
+
+    postFixup = ''
+      wrapPythonProgramsIn "$out/gui" "$out $pythonPath"
+    '';
+
+    doInstallCheck = true;
+    installCheckPhase = ''
+      "$out/gui/scyther.py" "$src/gui/Protocols/Demo/ns3.spdl"
+    '';
+  };
+in
+  buildEnv {
+    name = "scyther-${version}";
+    inherit meta;
+    paths = [ cli ] ++ lib.optional includeGUI gui;
+    pathsToLink = [ "/bin" ];
+
+    postBuild = ''
+      rm "$out/bin/scyther-linux"
+    '' + lib.optionalString includeProtocols ''
+      mkdir -p "$out/protocols"
+      cp -rv ${src}/protocols/* "$out/protocols"
+    '';
+  }