uboot: (firmwareOdroidC2/C4) don't invoke patch tool, use patches = [] instead

https://github.com/NixOS/nixpkgs/blob/master/pkgs/stdenv/generic/setup.sh#L948 this can do it nicely. Signed-off-by: Anton Arapov <anton@deadbeef.mx>
2021-04-03 12:58:10 +02:00 · 2021-04-03 12:58:10 +02:00 · 56de2bcd43
commit 56de2bcd43
30691 changed files with 3076956 additions and 0 deletions
--- a/pkgs/applications/science/misc/bada-bib/default.nix
+++ b/pkgs/applications/science/misc/bada-bib/default.nix
@ -0,0 +1,77 @@
+{ lib
+, meson
+, ninja
+, fetchFromGitHub
+, appstream-glib
+, desktop-file-utils
+, gdk-pixbuf
+, gettext
+, glib
+, gnome
+, gobject-introspection
+, gtk4
+, libxml2
+, pkg-config
+, python3Packages
+, wrapGAppsHook4 }:
+
+python3Packages.buildPythonApplication rec {
+  pname = "bada-bib";
+  version = "0.6.2";
+  format = "other";
+  strictDeps = false; # https://github.com/NixOS/nixpkgs/issues/56943
+
+  src = fetchFromGitHub {
+    owner = "RogerCrocker";
+    repo = "BadaBib";
+    rev = "refs/tags/v${version}";
+    sha256 = "sha256-3dXtBwqEqiXLjntmqLYeuwLv0RDb774+yOXc7vdf8+Y=";
+  };
+
+  nativeBuildInputs = [
+    gettext
+    gobject-introspection
+    libxml2
+    meson
+    ninja
+    pkg-config
+    wrapGAppsHook4
+  ];
+
+  buildInputs = [
+    gdk-pixbuf
+    glib
+    gtk4
+  ];
+
+  checkInputs = [
+    appstream-glib
+    desktop-file-utils
+  ];
+
+  pythonPath = with python3Packages; [
+    bibtexparser
+    pygobject3
+  ];
+
+  postPatch = ''
+    patchShebangs build-aux/meson/postinstall.py
+  '';
+
+  dontWrapGApps = true; # Needs python wrapper
+
+  preFixup = ''
+    makeWrapperArgs+=("''${gappsWrapperArgs[@]}")
+  '';
+
+  postFixup = ''
+    wrapPythonProgramsIn "$out/libexec" "$out $pythonPath"
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/RogerCrocker/BadaBib";
+    description = "A simple BibTeX Viewer and Editor";
+    maintainers = [ maintainers.Cogitri ];
+    license = licenses.gpl3Plus;
+  };
+}
--- a/pkgs/applications/science/misc/boinc/default.nix
+++ b/pkgs/applications/science/misc/boinc/default.nix
@ -0,0 +1,55 @@
+{ fetchFromGitHub, lib, stdenv, autoconf, automake, pkg-config, m4, curl,
+libGLU, libGL, libXmu, libXi, freeglut, libjpeg, libtool, wxGTK30, xcbutil,
+sqlite, gtk2, patchelf, libXScrnSaver, libnotify, libX11, libxcb }:
+
+let
+  majorVersion = "7.18";
+  minorVersion = "1";
+in
+
+stdenv.mkDerivation rec {
+  version = "${majorVersion}.${minorVersion}";
+  pname = "boinc";
+
+  src = fetchFromGitHub {
+    name = "${pname}-${version}-src";
+    owner = "BOINC";
+    repo = "boinc";
+    rev = "client_release/${majorVersion}/${version}";
+    sha256 = "sha256-ijkfWTFwwJXvh6f0P5hkzWODxU+Ugz6iQUK+5jEpWXQ=";
+  };
+
+  nativeBuildInputs = [ libtool automake autoconf m4 pkg-config ];
+
+  buildInputs = [
+    curl libGLU libGL libXmu libXi freeglut libjpeg wxGTK30 sqlite gtk2 libXScrnSaver
+    libnotify patchelf libX11 libxcb xcbutil
+  ];
+
+  NIX_LDFLAGS = "-lX11";
+
+  preConfigure = ''
+    ./_autosetup
+    configureFlags="$configureFlags --sysconfdir=$out/etc"
+  '';
+
+  enableParallelBuilding = true;
+
+  configureFlags = [ "--disable-server" ];
+
+  postInstall = ''
+    install --mode=444 -D 'client/scripts/boinc-client.service' "$out/etc/systemd/system/boinc.service"
+  '';
+
+  meta = with lib; {
+    description = "Free software for distributed and grid computing";
+    homepage = "https://boinc.berkeley.edu/";
+    license = licenses.lgpl2Plus;
+    platforms = platforms.linux;  # arbitrary choice
+    # checking for gcc options needed to detect all undeclared functions... cannot detect
+    # configure: error: in `/build/boinc-7.18.1-src':
+    # configure: error: cannot make gcc report undeclared builtins
+    broken = stdenv.isAarch64;
+    maintainers = with maintainers; [ Luflosi ];
+  };
+}
--- a/pkgs/applications/science/misc/colmap/default.nix
+++ b/pkgs/applications/science/misc/colmap/default.nix
@ -0,0 +1,53 @@
+{ mkDerivation, lib, fetchFromGitHub, cmake, boost17x, ceres-solver, eigen,
+  freeimage, glog, libGLU, glew, qtbase,
+  cudaSupport ? false, cudaPackages }:
+
+assert cudaSupport -> cudaPackages != { };
+
+let
+  boost_static = boost17x.override { enableStatic = true; };
+
+  # TODO: migrate to redist packages
+  inherit (cudaPackages) cudatoolkit;
+in
+mkDerivation rec {
+  version = "3.7";
+  pname = "colmap";
+  src = fetchFromGitHub {
+     owner = "colmap";
+     repo = "colmap";
+     rev = version;
+     hash = "sha256-uVAw6qwhpgIpHkXgxttKupU9zU+vD0Za0maw2Iv4x+I=";
+  };
+
+  # TODO: rm once the gcc11 issue is closed, https://github.com/colmap/colmap/issues/1418#issuecomment-1049305256
+  cmakeFlags = lib.optionals cudaSupport [
+    "-DCUDA_ENABLED=ON"
+    "-DCUDA_NVCC_FLAGS=--std=c++14"
+  ];
+
+  buildInputs = [
+    boost_static ceres-solver eigen
+    freeimage glog libGLU glew qtbase
+  ] ++ lib.optionals cudaSupport [
+    cudatoolkit
+  ];
+
+  nativeBuildInputs = [
+    cmake
+  ] ++ lib.optionals cudaSupport [
+    cudaPackages.autoAddOpenGLRunpathHook
+  ];
+
+  meta = with lib; {
+    description = "COLMAP - Structure-From-Motion and Multi-View Stereo pipeline";
+    longDescription = ''
+       COLMAP is a general-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline
+       with a graphical and command-line interface.
+    '';
+    homepage = "https://colmap.github.io/index.html";
+    license = licenses.bsd3;
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ lebastr ];
+  };
+}
--- a/pkgs/applications/science/misc/convertall/default.nix
+++ b/pkgs/applications/science/misc/convertall/default.nix
@ -0,0 +1,37 @@
+{ lib, stdenv, fetchFromGitHub, python3, wrapQtAppsHook }:
+
+let
+  inherit (python3.pkgs) wrapPython pyqt5;
+in stdenv.mkDerivation rec {
+  pname = "convertall";
+  version = "0.8.0";
+
+  src = fetchFromGitHub {
+    owner = "doug-101";
+    repo = "ConvertAll";
+    rev = "v${version}";
+    sha256 = "02xxasgbjbivsbhyfpn3cpv52lscdx5kc95s6ns1dvnmdg0fpng0";
+  };
+
+  nativeBuildInputs = [ python3 wrapPython wrapQtAppsHook ];
+
+  propagatedBuildInputs = [ pyqt5 ];
+
+  installPhase = ''
+    python3 install.py -p $out -x
+  '';
+
+  postFixup = ''
+    buildPythonPath $out
+    patchPythonScript $out/share/convertall/convertall.py
+    makeQtWrapper $out/share/convertall/convertall.py $out/bin/convertall
+  '';
+
+  meta = with lib; {
+    homepage = "https://convertall.bellz.org/";
+    description = "Graphical unit converter";
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ orivej ];
+    platforms = pyqt5.meta.platforms;
+  };
+}
--- a/pkgs/applications/science/misc/cwltool/default.nix
+++ b/pkgs/applications/science/misc/cwltool/default.nix
@ -0,0 +1,76 @@
+{ lib
+, fetchFromGitHub
+, git
+, nodejs
+, python3
+}:
+
+python3.pkgs.buildPythonApplication rec {
+  pname = "cwltool";
+  version = "3.1.20220224085855";
+  format = "setuptools";
+
+  src = fetchFromGitHub {
+    owner = "common-workflow-language";
+    repo = pname;
+    rev = version;
+    sha256 = "sha256-7+1xOV5Lodqtku0wX1urAEHsCcYKM3Vcd5RDg4DdVow=";
+  };
+
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace "ruamel.yaml >= 0.15, < 0.17.18" "ruamel.yaml" \
+      --replace "prov == 1.5.1" "prov" \
+      --replace "setup_requires=PYTEST_RUNNER," ""
+  '';
+
+  nativeBuildInputs = [
+    git
+  ];
+
+  propagatedBuildInputs = with python3.pkgs; [
+    argcomplete
+    bagit
+    coloredlogs
+    mypy-extensions
+    prov
+    psutil
+    pydot
+    rdflib
+    requests
+    ruamel-yaml
+    schema-salad
+    shellescape
+    typing-extensions
+  ];
+
+  checkInputs = with python3.pkgs; [
+    mock
+    nodejs
+    pytest-mock
+    pytest-xdist
+    pytestCheckHook
+  ];
+
+  disabledTests = [
+    "test_content_types"
+    "test_env_filtering"
+    "test_http_path_mapping"
+  ];
+
+  disabledTestPaths = [
+    "tests/test_udocker.py"
+    "tests/test_provenance.py"
+  ];
+
+  pythonImportsCheck = [
+    "cwltool"
+  ];
+
+  meta = with lib; {
+    description = "Common Workflow Language reference implementation";
+    homepage = "https://www.commonwl.org";
+    license = with licenses; [ asl20 ];
+    maintainers = with maintainers; [ veprbl ];
+  };
+}
--- a/pkgs/applications/science/misc/cytoscape/default.nix
+++ b/pkgs/applications/science/misc/cytoscape/default.nix
@ -0,0 +1,44 @@
+{ lib, stdenv, fetchurl, jre, makeWrapper, substituteAll, coreutils }:
+
+stdenv.mkDerivation rec {
+  pname = "cytoscape";
+  version = "3.9.1";
+
+  src = fetchurl {
+    url = "https://github.com/cytoscape/cytoscape/releases/download/${version}/${pname}-unix-${version}.tar.gz";
+    sha256 = "sha256-I4C2yGiIygnFUkRBC4LBSQFgjZlVKCoQGRphynVpscw=";
+  };
+
+  patches = [
+    # By default, gen_vmoptions.sh tries to store custom options in $out/share
+    # at run time. This patch makes sure $HOME is used instead.
+    (substituteAll {
+      src = ./gen_vmoptions_to_homedir.patch;
+      inherit coreutils;
+    })
+  ];
+
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ jre ];
+
+  installPhase = ''
+    mkdir -pv $out/{share,bin}
+    cp -Rv * $out/share/
+
+    ln -s $out/share/cytoscape.sh $out/bin/cytoscape
+
+    wrapProgram $out/share/cytoscape.sh \
+      --set JAVA_HOME "${jre}" \
+      --set JAVA  "${jre}/bin/java"
+
+    chmod +x $out/bin/cytoscape
+  '';
+
+  meta = {
+    homepage = "http://www.cytoscape.org";
+    description = "A general platform for complex network analysis and visualization";
+    license = lib.licenses.lgpl21;
+    maintainers = [lib.maintainers.mimame];
+    platforms = lib.platforms.unix;
+  };
+}
--- a/pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch
+++ b/pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch
@ -0,0 +1,19 @@
+diff -Nur a/gen_vmoptions.sh b/gen_vmoptions.sh
+--- a/gen_vmoptions.sh	2020-03-30 21:57:47.000000000 +0100
+++ b/gen_vmoptions.sh	2020-05-05 09:49:57.974989824 +0100
+@@ -1,13 +1,10 @@
+ #!/bin/sh
+ # Generates the Cytoscape.vmoptions file
+ 
+-script_path="$(dirname -- $0)"
+-
+-#vm_options_path="$HOME/.cytoscape"
+-vm_options_path=$script_path
+vm_options_path="$HOME/.cytoscape"
+ 
+ if [ ! -e $vm_options_path ]; then
+-    /bin/mkdir $vm_options_path
+    @coreutils@/bin/mkdir $vm_options_path
+ fi
+ 
+ # Determine amount of physical memory present:
--- a/pkgs/applications/science/misc/fityk/default.nix
+++ b/pkgs/applications/science/misc/fityk/default.nix
@ -0,0 +1,29 @@
+{ lib, stdenv, fetchFromGitHub, autoreconfHook, wxGTK30, boost, lua, zlib, bzip2
+, xylib, readline, gnuplot, swig3 }:
+
+stdenv.mkDerivation rec {
+  pname = "fityk";
+  version = "1.3.1";
+
+  src = fetchFromGitHub {
+    owner = "wojdyr";
+    repo = "fityk";
+    rev = "v${version}";
+    sha256 = "0kmrjjjwrh6xgw590awcd52b86kksmv6rfgih75zvpiavr1ygwsi";
+  };
+
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ wxGTK30 boost lua zlib bzip2 xylib readline
+    gnuplot swig3 ];
+
+  NIX_CFLAGS_COMPILE = [
+    "-std=c++11"
+  ];
+
+  meta = {
+    description = "Curve fitting and peak fitting software";
+    license = lib.licenses.gpl2;
+    homepage = "https://fityk.nieto.pl/";
+    platforms = lib.platforms.linux;
+  };
+}
--- a/pkgs/applications/science/misc/foldingathome/client.nix
+++ b/pkgs/applications/science/misc/foldingathome/client.nix
@ -0,0 +1,59 @@
+{ lib, stdenv
+, autoPatchelfHook
+, buildFHSUserEnv
+, dpkg
+, fetchurl
+, gcc-unwrapped
+, ocl-icd
+, zlib
+, extraPkgs ? []
+}:
+let
+  majMin = lib.versions.majorMinor version;
+  version = "7.6.13";
+
+  fahclient = stdenv.mkDerivation rec {
+    inherit version;
+    pname = "fahclient";
+
+    src = fetchurl {
+      url = "https://download.foldingathome.org/releases/public/release/fahclient/debian-stable-64bit/v${majMin}/fahclient_${version}_amd64.deb";
+      sha256 = "1j2cnsyassvifp6ymwd9kxwqw09hks24834gf7nljfncyy9g4g0i";
+    };
+
+    nativeBuildInputs = [
+      autoPatchelfHook
+      dpkg
+    ];
+
+    buildInputs = [
+      gcc-unwrapped.lib
+      zlib
+    ];
+
+    unpackPhase = "dpkg-deb -x ${src} ./";
+    installPhase = "cp -ar usr $out";
+  };
+in
+buildFHSUserEnv {
+  name = fahclient.name;
+
+  targetPkgs = pkgs': [
+    fahclient
+    ocl-icd
+  ] ++ extraPkgs;
+
+  runScript = "/bin/FAHClient";
+
+  extraInstallCommands = ''
+    mv $out/bin/$name $out/bin/FAHClient
+  '';
+
+  meta = {
+    description = "Folding@home client";
+    homepage = "https://foldingathome.org/";
+    license = lib.licenses.unfree;
+    maintainers = [ lib.maintainers.zimbatm ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
--- a/pkgs/applications/science/misc/foldingathome/control.nix
+++ b/pkgs/applications/science/misc/foldingathome/control.nix
@ -0,0 +1,58 @@
+{ lib, stdenv
+, autoPatchelfHook
+, dpkg
+, fahviewer
+, fetchurl
+, makeWrapper
+, python2
+}:
+let
+  majMin = lib.versions.majorMinor version;
+  version = "7.6.21";
+
+  python = python2.withPackages
+    (
+      ps: [
+        ps.pycairo
+        ps.pygobject2
+        ps.pygtk
+      ]
+    );
+in
+stdenv.mkDerivation rec {
+  inherit version;
+  pname = "fahcontrol";
+
+  src = fetchurl {
+    url = "https://download.foldingathome.org/releases/public/release/fahcontrol/debian-stable-64bit/v${majMin}/fahcontrol_${version}-1_all.deb";
+    sha256 = "1vfrdqkrvdlyxaw3f6z92w5dllrv6810lmf8yhcmjcwmphipvf71";
+  };
+
+  nativeBuildInputs = [
+    dpkg
+    makeWrapper
+  ];
+
+  buildInputs = [ fahviewer python ];
+
+  unpackPhase = ''
+    dpkg-deb -x ${src} ./
+  '';
+
+  installPhase = "cp -ar usr $out";
+
+  postFixup = ''
+    sed -e "s|/usr/bin|$out/bin|g" -i $out/share/applications/FAHControl.desktop
+    wrapProgram "$out/bin/FAHControl" \
+      --suffix PATH : "${fahviewer.outPath}/bin" \
+      --set PYTHONPATH "$out/lib/python2.7/dist-packages"
+  '';
+
+  meta = {
+    description = "Folding@home control";
+    homepage = "https://foldingathome.org/";
+    license = lib.licenses.unfree;
+    maintainers = [ lib.maintainers.zimbatm ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
--- a/pkgs/applications/science/misc/foldingathome/viewer.nix
+++ b/pkgs/applications/science/misc/foldingathome/viewer.nix
@ -0,0 +1,55 @@
+{ lib, stdenv
+, autoPatchelfHook
+, dpkg
+, fetchurl
+, freeglut
+, gcc-unwrapped
+, libGL
+, libGLU
+, makeWrapper
+, zlib
+}:
+let
+  majMin = lib.versions.majorMinor version;
+  version = "7.6.21";
+in
+stdenv.mkDerivation rec {
+  inherit version;
+  pname = "fahviewer";
+
+  src = fetchurl {
+    url = "https://download.foldingathome.org/releases/public/release/fahviewer/debian-stable-64bit/v${majMin}/fahviewer_${version}_amd64.deb";
+    sha256 = "00fd00pf6fcpplcaahvy9ir60mk69d9rcmwsyq3jrv9mxqm9aq7p";
+  };
+
+  nativeBuildInputs = [
+    autoPatchelfHook
+    dpkg
+    makeWrapper
+  ];
+
+  buildInputs = [
+    freeglut
+    gcc-unwrapped.lib
+    libGL
+    libGLU
+    zlib
+  ];
+
+  unpackPhase = ''
+    dpkg-deb -x ${src} ./
+    sed -e "s|/usr/bin|$out/bin|g" -i usr/share/applications/FAHViewer.desktop
+  '';
+
+  installPhase = ''
+    cp -ar usr $out
+  '';
+
+  meta = {
+    description = "Folding@home viewer";
+    homepage = "https://foldingathome.org/";
+    license = lib.licenses.unfree;
+    maintainers = [ lib.maintainers.zimbatm ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
--- a/pkgs/applications/science/misc/gephi/default.nix
+++ b/pkgs/applications/science/misc/gephi/default.nix
@ -0,0 +1,69 @@
+{ lib, stdenv, fetchFromGitHub, jdk, maven, javaPackages }:
+
+let
+  version = "0.9.2";
+
+  src = fetchFromGitHub {
+    owner = "gephi";
+    repo = "gephi";
+    rev = "v${version}";
+    sha256 = "0kqp2nvnsb55j1axb6hk0mlw5alyaiyb70z0mdybhpqqxyw2da2r";
+  };
+
+  # perform fake build to make a fixed-output derivation out of the files downloaded from maven central (120MB)
+  deps = stdenv.mkDerivation {
+    name = "gephi-${version}-deps";
+    inherit src;
+    buildInputs = [ jdk maven ];
+    buildPhase = ''
+      while mvn package -Dmaven.repo.local=$out/.m2 -Dmaven.wagon.rto=5000; [ $? = 1 ]; do
+        echo "timeout, restart maven to continue downloading"
+      done
+    '';
+    # keep only *.{pom,jar,sha1,nbm} and delete all ephemeral files with lastModified timestamps inside
+    installPhase = ''find $out/.m2 -type f -regex '.+\(\.lastUpdated\|resolver-status\.properties\|_remote\.repositories\)' -delete'';
+    outputHashAlgo = "sha256";
+    outputHashMode = "recursive";
+    outputHash = "1p7yf97dn0nvr005cbs6vdk3i341s8fya4kfccj8qqad2qgxflif";
+  };
+in
+stdenv.mkDerivation {
+  pname = "gephi";
+  inherit version;
+
+  inherit src;
+
+  buildInputs = [ jdk maven ];
+
+  buildPhase = ''
+    # 'maven.repo.local' must be writable so copy it out of nix store
+    mvn package --offline -Dmaven.repo.local=$(cp -dpR ${deps}/.m2 ./ && chmod +w -R .m2 && pwd)/.m2
+  '';
+
+  installPhase = ''
+    cp -r modules/application/target/gephi $out
+
+    # remove garbage
+    find $out -type f -name  .lastModified -delete
+    find $out -type f -regex '.+\.exe'     -delete
+
+    # use self-compiled JOGL to avoid patchelf'ing .so inside jars
+    rm $out/gephi/modules/ext/org.gephi.visualization/org-jogamp-{jogl,gluegen}/*.jar
+    cp ${javaPackages.jogl_2_3_2}/share/java/jogl*.jar $out/gephi/modules/ext/org.gephi.visualization/org-jogamp-jogl/
+    cp ${javaPackages.jogl_2_3_2}/share/java/glue*.jar $out/gephi/modules/ext/org.gephi.visualization/org-jogamp-gluegen/
+
+    echo "jdkhome=${jdk}" >> $out/etc/gephi.conf
+  '';
+
+  meta = with lib; {
+    description = "A platform for visualizing and manipulating large graphs";
+    homepage = "https://gephi.org";
+    sourceProvenance = with sourceTypes; [
+      fromSource
+      binaryBytecode  # deps
+    ];
+    license = licenses.gpl3;
+    maintainers = [ maintainers.taeer ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
--- a/pkgs/applications/science/misc/golly/default.nix
+++ b/pkgs/applications/science/misc/golly/default.nix
@ -0,0 +1,54 @@
+{lib, stdenv, fetchurl, wxGTK, perl, python3, zlib, libGLU, libGL, libX11, SDL2}:
+stdenv.mkDerivation rec {
+  pname = "golly";
+  version = "4.1";
+
+  src = fetchurl {
+    sha256 = "1j30dpzy6wh8fv1j2750hzc6wb0nhk83knl9fapccxgxw9n5lrbc";
+    url="mirror://sourceforge/project/golly/golly/golly-${version}/golly-${version}-src.tar.gz";
+  };
+
+  buildInputs = [
+    wxGTK perl python3 zlib libGLU libGL libX11 SDL2
+  ];
+
+  setSourceRoot = ''
+    sourceRoot=$(echo */gui-wx/)
+  '';
+
+  postPatch = ''
+    sed -e '/gollydir =/agollydir += "/../share/golly/";' -i wxgolly.cpp
+    grep share/golly wxgolly.cpp
+
+    sed -e 's@PYTHON_SHLIB@${python3}/lib/libpython3.so@' -i wxprefs.cpp
+    sed -e 's@PERL_SHLIB@'"$(find "${perl}/lib/" -name libperl.so)"'@' -i wxprefs.cpp
+    ! grep _SHLIB *.cpp
+
+    grep /lib/libpython wxprefs.cpp
+    grep /libperl wxprefs.cpp
+  '';
+
+  makeFlags=[
+    "-f" "makefile-gtk"
+    "ENABLE_SOUND=1" "ENABLE_PERL=1"
+  ];
+
+  installPhase = ''
+    mkdir -p "$out/bin"
+    cp ../golly ../bgolly "$out/bin"
+
+    mkdir -p "$out/share/doc/golly/"
+    cp ../docs/*  "$out/share/doc/golly/"
+
+    mkdir -p "$out/share/golly"
+    cp -r ../{Help,Patterns,Scripts,Rules} "$out/share/golly"
+  '';
+
+  meta = {
+    description = "Cellular automata simulation program";
+    license = lib.licenses.gpl2;
+    maintainers = [lib.maintainers.raskin];
+    platforms = lib.platforms.linux;
+    downloadPage = "https://sourceforge.net/projects/golly/files/golly";
+  };
+}
--- a/pkgs/applications/science/misc/gplates/default.nix
+++ b/pkgs/applications/science/misc/gplates/default.nix
@ -0,0 +1,71 @@
+{ lib
+, stdenv
+, mkDerivation
+, fetchurl
+, cmake
+, doxygen
+, graphviz
+, boost
+, cgal_5
+, gdal
+, glew
+, gmp
+, libGL
+, libGLU
+, mpfr
+, proj
+, python3
+, qtxmlpatterns
+, qwt
+}:
+
+let
+  python = python3.withPackages (ps: with ps; [
+    numpy
+  ]);
+  boost' = boost.override {
+    enablePython = true;
+    inherit python;
+  };
+  cgal = cgal_5.override {
+    boost = boost';
+  };
+in mkDerivation rec {
+  pname = "gplates";
+  version = "2.3.0";
+
+  src = fetchurl {
+    name = "gplates_${version}_src.tar.bz2";
+    url = "https://www.earthbyte.org/download/8421/?uid=b89bb31428";
+    sha256 = "0lrcmcxc924ixddii8cyglqlwwxvk7f00g4yzbss5i3fgcbh8n96";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    doxygen
+    graphviz
+  ];
+
+  buildInputs = [
+    boost'
+    cgal
+    gdal
+    glew
+    gmp
+    libGL
+    libGLU
+    mpfr
+    proj
+    python
+    qtxmlpatterns
+    qwt
+  ];
+
+  meta = with lib; {
+    description = "Desktop software for the interactive visualisation of plate-tectonics";
+    homepage = "https://www.gplates.org";
+    license = licenses.gpl2Only;
+    platforms = platforms.all;
+    broken = stdenv.isDarwin; # never built on Hydra https://hydra.nixos.org/job/nixpkgs/trunk/gplates.x86_64-darwin
+  };
+}
--- a/pkgs/applications/science/misc/graphia/default.nix
+++ b/pkgs/applications/science/misc/graphia/default.nix
@ -0,0 +1,35 @@
+{ stdenv, lib, cmake, fetchFromGitHub
+, wrapQtAppsHook, qtbase, qtquickcontrols2, qtgraphicaleffects
+}:
+
+stdenv.mkDerivation rec {
+  pname = "graphia";
+  version = "2.2";
+
+  src = fetchFromGitHub {
+    owner = "graphia-app";
+    repo = "graphia";
+    rev = version;
+    sha256 = "sha256:05givvvg743sawqy2vhljkfgn5v1s907sflsnsv11ddx6x51na1w";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    wrapQtAppsHook
+  ];
+  buildInputs = [
+    qtbase
+    qtquickcontrols2
+    qtgraphicaleffects
+  ];
+
+  meta = with lib; {
+    # never built on Hydra https://hydra.nixos.org/job/nixpkgs/trunk/graphia.x86_64-darwin
+    broken = (stdenv.isLinux && stdenv.isAarch64) || stdenv.isDarwin;
+    description = "A visualisation tool for the creation and analysis of graphs.";
+    homepage = "https://graphia.app";
+    license = licenses.gpl3Only;
+    maintainers = [ maintainers.bgamari ];
+    platforms = platforms.all;
+  };
+}
--- a/pkgs/applications/science/misc/megam/default.nix
+++ b/pkgs/applications/science/misc/megam/default.nix
@ -0,0 +1,47 @@
+{ fetchurl, lib, stdenv, ocaml, makeWrapper, ncurses }:
+
+let version = "0.92"; in
+stdenv.mkDerivation {
+  pname = "megam";
+  inherit 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 = lib.platforms.gnu ++ lib.platforms.linux;  # arbitrary choice
+  };
+}
--- a/pkgs/applications/science/misc/megam/ocaml-3.12.patch
+++ 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
+ 
--- a/pkgs/applications/science/misc/megam/ocaml-includes.patch
+++ 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 $(CAML_INCLUDES) 
+ 
+ ################ End of user's variables #####################
+ 
--- a/pkgs/applications/science/misc/netlogo/default.nix
+++ b/pkgs/applications/science/misc/netlogo/default.nix
@ -0,0 +1,59 @@
+{ jre, lib, stdenv, fetchurl, makeWrapper, makeDesktopItem }:
+
+let
+
+  desktopItem = makeDesktopItem rec {
+    name = "netlogo";
+    exec = name;
+    icon = name;
+    comment = "A multi-agent programmable modeling environment";
+    desktopName = "NetLogo";
+    categories = [ "Science" ];
+  };
+
+in
+
+stdenv.mkDerivation rec {
+  pname = "netlogo";
+  version = "6.1.1";
+
+  src = fetchurl {
+    url = "https://ccl.northwestern.edu/netlogo/${version}/NetLogo-${version}-64.tgz";
+    sha256 = "1j08df68pgggxqkmpzd369w4h97q0pivmmljdb48hjghx7hacblp";
+  };
+
+  src1 = fetchurl {
+    name = "netlogo.png";
+    url = "https://netlogoweb.org/assets/images/desktopicon.png";
+    sha256 = "1i43lhr31lzva8d2r0dxpcgr58x496gb5vmb0h2da137ayvifar8";
+  };
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  installPhase = ''
+    mkdir -pv $out/share/netlogo $out/share/icons/hicolor/256x256/apps $out/share/applications $out/share/doc
+    cp -rv app $out/share/netlogo
+    cp -v readme.md $out/share/doc/
+
+    # launcher with `cd` is required b/c otherwise the model library isn't usable
+    makeWrapper "${jre}/bin/java" "$out/bin/netlogo" \
+      --chdir "$out/share/netlogo/app" \
+      --add-flags "-jar netlogo-${version}.jar"
+
+    cp $src1 $out/share/icons/hicolor/256x256/apps/netlogo.png
+    cp ${desktopItem}/share/applications/* $out/share/applications
+  '';
+
+  meta = with lib; {
+    description = "A multi-agent programmable modeling environment";
+    longDescription = ''
+      NetLogo is a multi-agent programmable modeling environment. It is used by
+      many tens of thousands of students, teachers and researchers worldwide.
+    '';
+    homepage = "https://ccl.northwestern.edu/netlogo/index.shtml";
+    sourceProvenance = with sourceTypes; [ binaryBytecode ];
+    license = licenses.gpl2;
+    maintainers = [ maintainers.dpaetzel ];
+    platforms = platforms.linux;
+  };
+}
--- a/pkgs/applications/science/misc/nextinspace/default.nix
+++ b/pkgs/applications/science/misc/nextinspace/default.nix
@ -0,0 +1,44 @@
+{ lib
+, fetchFromGitHub
+, python3
+}:
+
+python3.pkgs.buildPythonApplication rec {
+  pname = "nextinspace";
+  version = "2.0.3";
+  format = "pyproject";
+
+  src = fetchFromGitHub {
+    owner = "not-stirred";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-Macx2pQglB95Bhc939TFVCHd1qvqJsco91EXKCIQLgg=";
+  };
+
+  nativeBuildInputs = with python3.pkgs; [
+    poetry-core
+  ];
+
+  pythonPath = with python3.pkgs; [
+    requests
+    tzlocal
+    colorama
+  ];
+
+  checkInputs = with python3.pkgs; [
+    pytest-lazy-fixture
+    pytestCheckHook
+    requests-mock
+  ];
+
+  pythonImportsCheck = [
+    "nextinspace"
+  ];
+
+  meta = with lib; {
+    description = "Print upcoming space-related events in your terminal";
+    homepage = "https://github.com/The-Kid-Gid/nextinspace";
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [ penguwin ];
+  };
+}
--- a/pkgs/applications/science/misc/openmodelica/combined/default.nix
+++ b/pkgs/applications/science/misc/openmodelica/combined/default.nix
@ -0,0 +1,30 @@
+{ stdenv, lib, openmodelica, symlinkJoin, gnumake, blas, lapack, makeWrapper }:
+symlinkJoin {
+  name = "openmodelica-combined";
+  paths = with openmodelica; [
+    omcompiler
+    omsimulator
+    omplot
+    omparser
+    omedit
+    omlibrary
+    omshell
+  ];
+
+  buildInputs = [ gnumake makeWrapper ];
+
+  postBuild = ''
+    wrapProgram $out/bin/OMEdit \
+      --prefix PATH : ${lib.makeBinPath [ gnumake stdenv.cc ]} \
+      --prefix LIBRARY_PATH : "${lib.makeLibraryPath [ blas lapack ]}" \
+      --set-default OPENMODELICALIBRARY "${openmodelica.omlibrary}/lib/omlibrary"
+  '';
+
+  meta = with lib; {
+    description = "An open-source Modelica-based modeling and simulation environment intended for industrial and academic usage";
+    homepage = "https://openmodelica.org";
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [ balodja smironov ];
+    platforms = platforms.linux;
+  };
+}
--- a/pkgs/applications/science/misc/openmodelica/default.nix
+++ b/pkgs/applications/science/misc/openmodelica/default.nix
@ -0,0 +1,17 @@
+{ lib, newScope, libsForQt5, clangStdenv }:
+lib.makeScope newScope (self:
+  let
+    callPackage = self.newScope { stdenv = clangStdenv; };
+    callQtPackage = self.newScope (libsForQt5 // { stdenv = clangStdenv; });
+  in
+  {
+    mkOpenModelicaDerivation = callPackage ./mkderivation { };
+    omcompiler = callPackage ./omcompiler { };
+    omplot = callQtPackage ./omplot { };
+    omsimulator = callPackage ./omsimulator { };
+    omparser = callPackage ./omparser { };
+    omedit = callQtPackage ./omedit { };
+    omlibrary = callPackage ./omlibrary { };
+    omshell = callQtPackage ./omshell { };
+    combined = callPackage ./combined { };
+  })
--- a/pkgs/applications/science/misc/openmodelica/mkderivation/default.nix
+++ b/pkgs/applications/science/misc/openmodelica/mkderivation/default.nix
@ -0,0 +1,101 @@
+# mkOpenModelicaDerivation is an mkDerivation function for packages
+# from OpenModelica suite.
+
+{ stdenv, lib, fetchgit, autoconf, automake, libtool, cmake, autoreconfHook, symlinkJoin }:
+pkg:
+let
+  inherit (builtins) hasAttr getAttr length elemAt;
+  inherit (lib) attrByPath concatStringsSep;
+
+
+  # A few helpers functions:
+
+  # getAttrDef is just a getAttr with default fallback
+  getAttrDef = attr: default: x: attrByPath [ attr ] default x;
+
+  # getAttr-like helper for optional append to string:
+  # "Hello" + appendByAttr "a" " " {a = "world";} = "Hello world"
+  # "Hello" + appendByAttr "a" " " {} = "Hello"
+  appendByAttr = attr: sep: x: if hasAttr attr x then sep + (getAttr attr x) else "";
+
+  # Are there any OM dependencies at all?
+  ifDeps = length pkg.omdeps != 0;
+
+  # Dependencies of current OpenModelica-target joined in one file tree.
+  # Return the dep itself in case it is a single one.
+  joinedDeps =
+    if length pkg.omdeps == 1
+    then elemAt pkg.omdeps 0
+    else
+      symlinkJoin {
+        name = pkg.pname + "-omhome";
+        paths = pkg.omdeps;
+      };
+
+  # Should we run ./configure for the target pkg?
+  omautoconf = getAttrDef "omautoconf" false pkg;
+
+  # Name of the make target
+  omtarget = getAttrDef "omtarget" pkg.pname pkg;
+
+  # Directory of target sources
+  omdir = getAttrDef "omdir" pkg.pname pkg;
+
+  # Simple to to m4 configuration scripts
+  postPatch = lib.optionalString ifDeps ''
+    sed -i ''$(find -name omhome.m4) -e 's|if test ! -z "$USINGPRESETBUILDDIR"|if test ! -z "$USINGPRESETBUILDDIR" -a -z "$OMHOME"|'
+  '' +
+  appendByAttr "postPatch" "\n" pkg;
+
+  # Update shebangs in the scripts before running configuration.
+  preAutoreconf = "patchShebangs --build common" +
+    appendByAttr "preAutoreconf" "\n" pkg;
+
+  # Tell OpenModelica where built dependencies are located.
+  configureFlags = lib.optional ifDeps "--with-openmodelicahome=${joinedDeps}" ++
+    getAttrDef "configureFlags" [ ] pkg;
+
+  # Our own configurePhase that accounts for omautoconf
+  configurePhase = ''
+    runHook preConfigure
+    export configureFlags="''${configureFlags} --with-ombuilddir=$PWD/build --prefix=$prefix"
+    ./configure --no-recursion $configureFlags
+    ${lib.optionalString omautoconf "(cd ${omdir}; ./configure $configureFlags)"}
+    runHook postConfigure
+  '';
+
+  # Targets that we want to build ourselves:
+  deptargets = lib.forEach pkg.omdeps (dep: dep.omtarget);
+
+  # ... so we ask openmodelica makefile to skip those targets.
+  preBuild = ''
+    for target in ${concatStringsSep " " deptargets}; do
+      touch ''${target}.skip;
+    done
+  '' +
+  appendByAttr "preBuild" "\n" pkg;
+
+  makeFlags = "${omtarget}" +
+    appendByAttr "makeFlags" " " pkg;
+
+  installFlags = "-i " +
+    appendByAttr "installFlags" " " pkg;
+
+
+in
+stdenv.mkDerivation (pkg // {
+  inherit omtarget postPatch preAutoreconf configureFlags configurePhase preBuild makeFlags installFlags;
+
+  src = fetchgit (import ./src-main.nix);
+  version = "1.18.0";
+
+  nativeBuildInputs = getAttrDef "nativeBuildInputs" [ ] pkg
+    ++ [ autoconf automake libtool cmake autoreconfHook ];
+
+  buildInputs = getAttrDef "buildInputs" [ ] pkg
+    ++ lib.optional ifDeps joinedDeps;
+
+  dontUseCmakeConfigure = true;
+
+  hardeningDisable = [ "format" ];
+})
--- a/pkgs/applications/science/misc/openmodelica/mkderivation/src-main.nix
+++ b/pkgs/applications/science/misc/openmodelica/mkderivation/src-main.nix
@ -0,0 +1,7 @@
+{
+  url = "https://github.com/OpenModelica/OpenModelica/";
+  rev = "49be4faa5a625a18efbbd74cc2f5be86aeea37bb";
+  sha256 = "0klqiy4sdizl1djb9hb0arcvfcjz2mmnakrjx81mmxcbr8yq2016";
+  fetchSubmodules = true;
+}
+# Update with: nix run -f ./nixpkgs/default.nix nix-prefetch-git -c nix-prefetch-git 'https://github.com/OpenModelica/OpenModelica/' 'v1.18.0' --fetch-submodules
--- a/pkgs/applications/science/misc/openmodelica/omcompiler/default.nix
+++ b/pkgs/applications/science/misc/openmodelica/omcompiler/default.nix
@ -0,0 +1,63 @@
+{ stdenv
+, lib
+, gfortran
+, flex
+, bison
+, jre8
+, blas
+, lapack
+, curl
+, readline
+, expat
+, pkg-config
+, buildPackages
+, targetPackages
+, libffi
+, binutils
+, mkOpenModelicaDerivation
+}:
+let
+  isCross = stdenv.buildPlatform != stdenv.hostPlatform;
+  nativeOMCompiler = buildPackages.openmodelica.omcompiler;
+in
+mkOpenModelicaDerivation ({
+  pname = "omcompiler";
+  omtarget = "omc";
+  omdir = "OMCompiler";
+  omdeps = [ ];
+  omautoconf = true;
+
+  nativeBuildInputs = [
+    jre8
+    gfortran
+    flex
+    bison
+    pkg-config
+  ] ++ lib.optional isCross nativeOMCompiler;
+
+  buildInputs = [ targetPackages.stdenv.cc.cc blas lapack curl readline expat libffi binutils ];
+
+  postPatch = ''
+    sed -i -e '/^\s*AR=ar$/ s/ar/${stdenv.cc.targetPrefix}ar/
+               /^\s*ar / s/ar /${stdenv.cc.targetPrefix}ar /
+               /^\s*ranlib/ s/ranlib /${stdenv.cc.targetPrefix}ranlib /' \
+        $(find ./OMCompiler -name 'Makefile*')
+  '';
+
+  preFixup = ''
+    for entry in $(find $out -name libipopt.so); do
+      patchelf --shrink-rpath --allowed-rpath-prefixes /nix/store $entry
+      patchelf --set-rpath '$ORIGIN':"$(patchelf --print-rpath $entry)" $entry
+    done
+  '';
+
+  meta = with lib; {
+    description = "Modelica compiler from OpenModelica suite";
+    homepage = "https://openmodelica.org";
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [ balodja smironov ];
+    platforms = platforms.linux;
+  };
+} // lib.optionalAttrs isCross {
+  configureFlags = [ "--with-omc=${nativeOMCompiler}/bin/omc" ];
+})
--- a/pkgs/applications/science/misc/openmodelica/omedit/default.nix
+++ b/pkgs/applications/science/misc/openmodelica/omedit/default.nix
@ -0,0 +1,38 @@
+{ lib
+, jre8
+, qmake
+, qtbase
+, qttools
+, qtwebkit
+, qtxmlpatterns
+, binutils
+, wrapQtAppsHook
+, openmodelica
+, mkOpenModelicaDerivation
+}:
+with openmodelica;
+mkOpenModelicaDerivation rec {
+  pname = "omedit";
+  omdir = "OMEdit";
+  omdeps = [ omcompiler omplot omparser omsimulator ];
+  omautoconf = true;
+
+  nativeBuildInputs = [ jre8 qmake qtbase qttools wrapQtAppsHook ];
+
+  buildInputs = [ qtwebkit qtxmlpatterns binutils ];
+
+  postPatch = ''
+    sed -i ''$(find -name qmake.m4) -e '/^\s*LRELEASE=/ s|LRELEASE=.*$|LRELEASE=${lib.getDev qttools}/bin/lrelease|'
+  '';
+
+  dontUseQmakeConfigure = true;
+  QMAKESPEC = "linux-clang";
+
+  meta = with lib; {
+    description = "A Modelica connection editor for OpenModelica";
+    homepage = "https://openmodelica.org";
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [ balodja smironov ];
+    platforms = platforms.linux;
+  };
+}
--- a/pkgs/applications/science/misc/openmodelica/omlibrary/default.nix
+++ b/pkgs/applications/science/misc/openmodelica/omlibrary/default.nix
@ -0,0 +1,37 @@
+{ lib
+, stdenv
+, fetchgit
+, bash
+, pkg-config
+, jre8
+, libuuid
+, openmodelica
+, mkOpenModelicaDerivation
+}:
+let
+  fakegit = import ./fakegit.nix { inherit lib stdenv fetchgit bash; };
+in
+mkOpenModelicaDerivation {
+  pname = "omlibrary";
+  omdir = "libraries";
+  omtarget = "omlibrary-all";
+  omdeps = [ openmodelica.omcompiler ];
+
+  postPatch = ''
+    patchShebangs --build libraries
+    cp -fv ${fakegit}/bin/checkout-git.sh libraries/checkout-git.sh
+
+    # The EMOTH library is broken in OpenModelica 1.17.0
+    # Let's remove it from targets.
+    sed -i -e '/^OTHER_LIBS=/ s/EMOTH //' libraries/Makefile.libs
+  '';
+
+  meta = with lib; {
+    description = "A collection of Modelica libraries to use with OpenModelica,
+including Modelica Standard Library";
+    homepage = "https://openmodelica.org";
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [ balodja smironov ];
+    platforms = platforms.linux;
+  };
+}
--- a/pkgs/applications/science/misc/openmodelica/omlibrary/fakegit.nix
+++ b/pkgs/applications/science/misc/openmodelica/omlibrary/fakegit.nix
@ -0,0 +1,49 @@
+{ lib, stdenv, fetchgit, bash }:
+let
+  mkscript = path: text: ''
+    mkdir -pv `dirname ${path}`
+    cat > ${path} <<"EOF"
+    #!${bash}/bin/bash
+    ME=$(basename ${path})
+    ${text}
+    EOF
+    sed -i "s@%out@$out@g" ${path}
+    chmod +x ${path}
+  '';
+
+  hashname = r:
+    let
+      rpl = lib.replaceChars [ ":" "/" ] [ "_" "_" ];
+    in
+    (rpl r.url) + "-" + (rpl r.rev);
+
+in
+stdenv.mkDerivation {
+  name = "fakegit";
+
+  buildCommand = ''
+    mkdir -pv $out/repos
+    ${lib.concatMapStrings
+      (r: "cp -r ${fetchgit r} $out/repos/${hashname r}\n")
+      (import ./src-libs.nix)}
+
+    ${mkscript "$out/bin/checkout-git.sh" ''
+      if test "$#" -ne 4; then
+        echo "Usage: $0 DESTINATION URL GITBRANCH HASH"
+        exit 1
+      fi
+      DEST=$1
+      URL=`echo $2 | tr :/ __`
+      GITBRANCH=$3
+      REVISION=$4
+
+      REVISION=`echo $REVISION | tr :/ __`
+
+      rm -rf $DEST
+      mkdir -pv $DEST
+      echo "FAKEGIT cp -r %out/repos/$URL-$REVISION $DEST" >&2
+      cp -r %out/repos/$URL-$REVISION/* $DEST
+      chmod u+w -R $DEST
+    ''}
+  '';
+}
--- a/pkgs/applications/science/misc/openmodelica/omlibrary/src-libs.nix
+++ b/pkgs/applications/science/misc/openmodelica/omlibrary/src-libs.nix
@ -0,0 +1,81 @@
+[
+{ url = "https://github.com/modelica-3rdparty/AdvancedNoise.git"; rev = "5ce57acd279dadd0d25b76a6b02d3f9e9d061246"; sha256 = "07jjbj0y6bak269md3xniqb5lgc33m92ar5qixqxj5yxdjaahfs2"; fetchSubmodules = true; }
+{ url = "https://github.com/RWTH-EBC/AixLib.git"; rev = "65e49ddf5c935846888a61aa303e52c909619079"; sha256 = "18xn8j3x3j4x9bpjgqnq0b6p3yzzsg5n62fv1ldqbbjcmi0vimd5"; fetchSubmodules = true; }
+{ url = "https://github.com/RWTH-EBC/AixLib.git"; rev = "v0.4.0"; sha256 = "0dw34mjq29n55xh51g1c9a9d0d8gbpn16gj309dfxn4v2hbnfvzx"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/AlgebraTestSuite.git"; rev = "b937e1a7f447138c59abec9b2092f84f16bf02e8"; sha256 = "0406inasx61dk7vcnziiyhxkna7g61a5hn0znnbxj817hz6q11zn"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/ApproxSpline.git"; rev = "28420f5c1a88c9cd069defbd8c05e4a78a090675"; sha256 = "07gpyi2brj5zpvrlsnflqjnhbrgxvpqbdshp8lp4lh9mnj5jv95d"; fetchSubmodules = true; }
+{ url = "https://github.com/OpenModelica/BioChem.git"; rev = "v1.0.2"; sha256 = "037bvj2lqrslg8k5r0rjgdzccslj9bj25b55k4g440vabm5p05qm"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/BondGraph.git"; rev = "20c23e60d12989bd4668ccac47659d82d39d29cc"; sha256 = "0yrkk708v4bvf423xb4zgpmnaj8qhq5primdg758ayddgli23wa9"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/BrineProp.git"; rev = "834fb3519ca8f89efe268582d39d00a7c3991150"; sha256 = "1iwqh4kr36wgxc0gci63gdgbqln2sap1w4bkydk1vkss2s302lg4"; fetchSubmodules = true; }
+{ url = "https://github.com/EDF-TREE/BuildSysPro.git"; rev = "v3.3.0"; sha256 = "1cvcany3q9p1xndarxa2d8mmqxdnqk22476q8l61nayz5qy25x61"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/BuildingControlLib.git"; rev = "v1.0.0"; sha256 = "0ckdxway0m755mbrl94k4458sijzgknlzsrf7xs5bjymxchm8r2m"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/BuildingSystems.git"; rev = "c3070d48015ee75c1577f349cb388a498bef7270"; sha256 = "0r876wm6f1xx4cli1lqlylpl3zgaddmy06hcafbnzry9j38vbz4y"; fetchSubmodules = true; }
+{ url = "https://github.com/lbl-srg/modelica-buildings.git"; rev = "v6.0.0"; sha256 = "0rnnk1clji0myzr7adggki6knbl6v8381vwnqgiz8mkxbmzdwm4f"; fetchSubmodules = true; }
+{ url = "https://github.com/lbl-srg/modelica-buildings.git"; rev = "v7.0.0"; sha256 = "04n04pp4zvyg8n8h7h79c3wyk7lmn940mh7qzs0lv76g1ybypnlz"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/Chemical.git"; rev = "5645573fced862430b7b598b4d7ec1a39c7aa0fa"; sha256 = "1kh7kpmjfz55pb8553srlnrh8l00nw21xf5mjzh7nx9b1rndnmyg"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/DeployStructLib.git"; rev = "v1.0"; sha256 = "1k4zw9lnd0javw4zigxc15l58yf7xdz36b7808g65qxy89w6ksr2"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/DisHeatLib.git"; rev = "b11f53379c122870a52f2da9b1705d2c911cd21d"; sha256 = "1vm96a4z0b40r0nisxrrzyvan4yphjdkx4ad655phva2636xb5rr"; fetchSubmodules = true; }
+{ url = "https://github.com/AHaumer/DriveControl.git"; rev = "b7233fd97a92867bb4ec2c3647c7f7e888398644"; sha256 = "0nyp1n8wrkjzfypsmjjzac0g9p4wbc1cxxr040fj20bqdg9l3h1b"; fetchSubmodules = true; }
+{ url = "https://github.com/christiankral/ElectroMechanicalDrives.git"; rev = "v2.2.0"; sha256 = "0012phmn1y9fgpph45lwbjk0yhm5czidf2z6khm8lddvk93wf31b"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/ExternData.git"; rev = "v2.5.0"; sha256 = "19dsyq1mk5vl54fqaffzqafm5w94l011cy7pg16c7i933dbqnkki"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica/ExternalMedia.git"; rev = "6138312c96142ff3c01190147e6277991bfa2fca"; sha256 = "1d9g2hbdvgz13j7kdi1kglkkllj9f00x3dwdp5piyypvs464jsn5"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/ExternalMemoryLib.git"; rev = "6488d5815bda23c665123baa916789e283e16d2c"; sha256 = "06y1i5w690b3b9x23nzls8y67fl7yd7bn4xl5j0dmyi4qx33aqda"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/FMITest.git"; rev = "a67a276083f4010b249802ad8fc70dc30c09adfd"; sha256 = "0mg8jlvlwql2nsjiy7c3rdibv73bkfk149ac0450d5pc0hfn9mln"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/FailureModes.git"; rev = "v1.2.1"; sha256 = "1z8bwrld1rkydgssab5gnrd76frrbky8qxi1lvlaf2jidj6bzn1l"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/FaultTriggering.git"; rev = "v0.6.6"; sha256 = "0a08yyrbg4a49s0bgqgyds6pidx9xr47yspvl9bdak1mq34qibip"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/FeedDriveLibrary.git"; rev = "1.0.1"; sha256 = "15fi9dj6zgl0fr90cwxqjbpphj0dwrrmk74hf25j6zd85w2ycqdz"; fetchSubmodules = true; }
+{ url = "https://github.com/DLR-SR/FractionalOrder.git"; rev = "99918820e346c362c3ad52d782c8215e5deeac4c"; sha256 = "1pycss6fqh86frfdbdfffjhaz09fz1558f9azgckhf8drx6ry1qs"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/Greenhouses-Library.git"; rev = "89ae0e8097eb0751abce2013d304fa5f9c09b885"; sha256 = "1q77xj6aysqsn3d7kjmcq7dihbw18iqm35ifzdi75xgf3cgwla4f"; fetchSubmodules = true; }
+{ url = "https://github.com/christiankral/HanserModelica.git"; rev = "v1.1.0"; sha256 = "0zwkrhg2y42m18p4z51izrickiv1vikgz0z7fpjia4dbppckav8i"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/HelmholtzMedia.git"; rev = "3b4a4bca94d388744b2d045344ea2f9b0b4d405b"; sha256 = "17fzpan89075vb5vbhw5ylgxcdsmj2vjnmmka7cgzh06izb69nvh"; fetchSubmodules = true; }
+{ url = "https://github.com/ibpsa/modelica-ibpsa.git"; rev = "v3.0.0"; sha256 = "0xwgfndlw76zfmiiqadl85l9na9igsqlmfcawx526sdw2lhhgics"; fetchSubmodules = true; }
+{ url = "https://github.com/open-ideas/IDEAS.git"; rev = "v2.1.0"; sha256 = "0xp0zg6ib5536d5vl361lsn5w5faqdf6djhcmfxns629wjima8rn"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/IndustrialControlSystems.git"; rev = "v1.1.0"; sha256 = "1nvgx94iy1pws0768anrl7ssjlzslb5mbp21j7xvf6wpqfmj0npc"; fetchSubmodules = true; }
+{ url = "https://github.com/christiankral/KeyWordIO.git"; rev = "v0.9.0"; sha256 = "10kvj6zn2r6m3403ja8nkkxbfcchkz0pfk3g70ibr76zivxb5nim"; fetchSubmodules = true; }
+{ url = "https://github.com/FishSim/LibRAS.git"; rev = "fca9de50a484a2213f3ca1b39e275c237c471688"; sha256 = "0w1c87sifq8klq0f2l70qxjrlvahyxy1cx9rln80rni4d427yc1k"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/LinearMPC.git"; rev = "v1.0"; sha256 = "1crj60i5f33l9pgip0xbv6ankcga7px0644cj7c2wnzn1fjmn2k8"; fetchSubmodules = true; }
+{ url = "https://github.com/looms-polimi/MEV.git"; rev = "v1.0.1"; sha256 = "1a7ih9lc01wzaq8a8aznggpi4aqnczyzq49q5hc4fqvmfwl7l0j3"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/ModPowerSystems.git"; rev = "df3afce27d5e935c4111f392275744a655abe216"; sha256 = "1b1fikm92lv6gj82imka3hxbjwv04i4h33y69yhcxdpqa6z6hm4z"; fetchSubmodules = true; }
+{ url = "https://github.com/OpenModelica/OpenModelica-ModelicaStandardLibrary.git"; rev = "4a91d52248b0f17415bba1d58881fc730bd94215"; sha256 = "19caxz6hvlrsls3b2387a24zwwnykbb138jpb42gwpy8jlh93yzi"; fetchSubmodules = true; }
+{ url = "https://github.com/OpenModelica/OpenModelica-ModelicaStandardLibrary.git"; rev = "cab27240a4a3ed4ea137226f056bbc0d79543f7a"; sha256 = "06y911i2hs7hg4ykhb8wngvxhwnaww8rsakwa7ssd047a7glzsb0"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/Modelica-Arduino.git"; rev = "v0.1.0"; sha256 = "1n34dksqhrn1synv2mp2ifk4dxyhp15f5v1jb1b3dbw9n19951qb"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/Modelica-GNU_ScientificLibrary.git"; rev = "9235ab28bdd7f0fe3e7abba48af53d73332858ec"; sha256 = "168g9gg12lfa863ifs41bnx6yd0yyjnal6986dgpm51dj5arw6id"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/Modelica-MVEM.git"; rev = "v1.0.1"; sha256 = "1p68691dnl06lgwm4bl9g036brn4vl7m5x3gq4rxc291339frixk"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/ModelicaADS.git"; rev = "v1.0.1"; sha256 = "0fhxrl07d7v3wa79d30psm1gxydc0p7s2akfirdx6dai0633skp9"; fetchSubmodules = true; }
+{ url = "https://github.com/xogeny/ModelicaBook.git"; rev = "v0.6.0"; sha256 = "0yqbll6p738yvpi1x11cjngpz2glda07mljrkjlm23p7l53x63dc"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-compliance/compliance.git"; rev = "8a91e75d8a26acc4de30fc0e5d5e9db83c970bd6"; sha256 = "1cym1wlgsvfrryq8zqzzrgs4wam1l7pc20q07hk3d615nhq21lg6"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/ModelicaDFR.git"; rev = "37a441934d05330cf3d13e9ec551954d27eca84c"; sha256 = "13rpcs8cl9x15vi655150zmhmg1iaxpzvxrl3rqif46zpl5dhlj2"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica/Modelica_DeviceDrivers.git"; rev = "v1.8.2"; sha256 = "16c0p9zn0qrraz59ivinibmikdd251plm1vqngznzhksjwvz6bja"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica/Modelica_LinearSystems2.git"; rev = "v2.3.5"; sha256 = "0rzicynqgayydxqynnairxk7ybg4alv1xnfz8cgkrpicl2g9bacg"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/Modelica_Requirements.git"; rev = "a427b5cb7997e9036c577d219e6b8a5d0c28389a"; sha256 = "1ihx46kifnfi9kw1g8nmd9sarl766whbzdk6a44alczsya4gg45k"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica/Modelica_Synchronous.git"; rev = "c8350276bfd945086962cf4150ba941b9c57ed13"; sha256 = "12ad7fpjy50ky3lvl65r9d5xvlzvw5yqdnbp4rsgl3qw7s3wrmja"; fetchSubmodules = true; }
+{ url = "https://github.com/jwindahlModelon/MultiPhaseMixtureMedia.git"; rev = "0bda0c58af6384f8e0edf7aa7520afb369af3e38"; sha256 = "11bqm69504bh4h05dxlwdmjfxwls06mr49cz47kl8jmrygkfi4i2"; fetchSubmodules = true; }
+{ url = "https://github.com/OpenIPSL/OpenIPSL.git"; rev = "v1.5.0"; sha256 = "09xrcz0rdxdy220ki5zyl7920y0a4lg24p0aibna4ad15vszhhwj"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/Optimisers.git"; rev = "e33c69edaad6dad8029167b0ca00533964a6fe37"; sha256 = "0hcxsrr2n4fzaxdjvgvqayz38kpfk86cclvg5pzcfmjc5bznb8bs"; fetchSubmodules = true; }
+{ url = "https://github.com/lochel/PNlib.git"; rev = "059545d48dd9ceeccfa3b4e47689ec8dd334dcd8"; sha256 = "1a0hxkgsi4klw9c8zav1dy2p1c85ald29gx82hfacwv55xl9f127"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/PVSystems.git"; rev = "v0.6.2"; sha256 = "0vcgvdaqfbn46lpzk0kvsif3d55wf8yzhkbdpf5zv04kv7zw25w9"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/PhotoVoltaics.git"; rev = "v1.6.0"; sha256 = "0zqx77z217iln3vfxn2v3c2jl0jz5kgcd96ylvimjnwr30mxr09n"; fetchSubmodules = true; }
+{ url = "https://github.com/MarekMatejak/Physiolibrary.git"; rev = "v2.3.1"; sha256 = "0nxfw63m278gaff18zz29n2s1vk4kwdbv2qvbjmcq86fl1i5b3bg"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/Physiomodel.git"; rev = "v1.0.0"; sha256 = "1sdhv5qgjqv3zdq57pkkrh04ainwv9n5zqd8mb9a3ybjmwdjf6f9"; fetchSubmodules = true; }
+{ url = "https://github.com/dzimmer/PlanarMechanics.git"; rev = "55224a9e76de8aa7f708236bd4d7dee624ecba50"; sha256 = "0hf7vi44adss86x5ahk5if7bdjgw773d8mb3d8ianq12g8azycyd"; fetchSubmodules = true; }
+{ url = "https://github.com/PowerGrids/PowerGrids.git"; rev = "v1.0.0"; sha256 = "06bx8mqvmizhfwg99djdfgh2mblc4wzmg0zq4ilrp586jwfninmz"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica/PowerSystems.git"; rev = "v1.0.0"; sha256 = "1xwhwich7gi6vl33zl2r78xdjklchgkjcnvww6390j20l1wjznkn"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica/PowerSystems.git"; rev = "f0721333f4875143565147a7d043bee1c300873b"; sha256 = "0gbvx0gzf3akb0w7yvdxfq2y4ps91cy5b93iwnvnw7652x716813"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/RealTimeCoordinationLibrary.git"; rev = "v1.0.2"; sha256 = "0ch4la04hm059ii5wzph9gsbvqhnfqrvvpqi57qn27bm10c4la0m"; fetchSubmodules = true; }
+{ url = "https://github.com/casella/ScalableTestSuite.git"; rev = "v1.11.5"; sha256 = "0bhj1q9b8d29nrbr253zszy1w1yvyizvyr3law1pqjj6mhbqmg4i"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/Servomechanisms.git"; rev = "3bf82ba5d3f31b4a0ae05f99ae690037358e153e"; sha256 = "1swka7d58wkg5pqv59lqgfi7gv6rg5vra4j6r76pn9czx9ddal8w"; fetchSubmodules = true; }
+{ url = "https://github.com/SolarTherm/SolarTherm.git"; rev = "203fb5af3b95c731c7fcbe2833d51fd420e80796"; sha256 = "1bh4y4igzd0k59xm8j14p52gnlbwkiwwy6bhhyarpr361yrchn33"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/Soltermica.git"; rev = "9f7224bd89335f95dffe1ccdaa094df5a3279fdf"; sha256 = "1bif3cnwjas6x7b8ahwkm7dbrqrfdqwwa26zmdc6zrpfncl3kqd0"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/SystemDynamics.git"; rev = "2f6bd9382c5aac2aff9148cd9113a418767734b6"; sha256 = "0ii2mj6ngwjir3gzyad8wsj86pvd6wzal91nz2y7gzwj1djchb3x"; fetchSubmodules = true; }
+{ url = "https://github.com/thom-marx/ThermalSeparation.git"; rev = "ffa0495ba829ecab105be4bfb3b7652625ec9c03"; sha256 = "1czm97bcrpp2jv0a0kd31a929wqlrlzdhdxvyy4w499dn20jzv1l"; fetchSubmodules = true; }
+{ url = "https://github.com/casella/ThermoPower.git"; rev = "650be2c8cbd5abc3535e92b865e509073afc8aeb"; sha256 = "08ijrx8xw43dadz5s3kiwa17ax9faq2wyq9gm0vlz9ddbkj0hcaq"; fetchSubmodules = true; }
+{ url = "https://openmodelica.org/git/ThermoSysPro.git"; rev = "db81ae1b5a6a85f6c6c7693244cafa6087e18ff5"; sha256 = "12fsf0xxxc1ja6vmm9ff85f8j5sg1lb7w4g57s2w3fkf4d3a7d0c"; fetchSubmodules = true; }
+{ url = "https://openmodelica.org/git/ThermoSysPro.git"; rev = "5cef9acb4dedf8af6f4638a4448f08a544ebd30b"; sha256 = "0ihnz1s4rs42yis9zym9nw29ia2lqz2yx2wblc50p6f221w7q78s"; fetchSubmodules = true; }
+{ url = "https://github.com/lenaRB/VVDRlib.git"; rev = "eae4981674642eddffc7f2aa3690320fcaddee0e"; sha256 = "0qxxk2xlas5mqyc1h8ndic208qj1sm5mr5y8664kv3py7i8jdqi4"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica/VehicleInterfaces.git"; rev = "v1.2.5"; sha256 = "044k17cpc88wprrvw03p6crm6dy6x9a6xj5104d5nln71lqz5sdq"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/WasteWater.git"; rev = "v2.1.0"; sha256 = "1dxr4m9j7b5266daj4klbrhvnkqr73sximdw9bk9v5qf0s28li99"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/WindPowerPlants.git"; rev = "v1.2.0"; sha256 = "1lyrqwsb6sm1wc7vlj72zk5cpjhhzh27fviiqayddqy2b903xish"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/ipsl.git"; rev = "v1.1.1"; sha256 = "1w2iah8c5d8n01wmxydjk0rrcxh88g8yjy2zmv403azcccq7byzp"; fetchSubmodules = true; }
+{ url = "https://github.com/modelica-3rdparty/netCDF-DataReader.git"; rev = "v2.5.0"; sha256 = "1pd5xf5bgz010lryv8bj6lvlfqn9p184csiffwj8icx7rycnlcqb"; fetchSubmodules = true; }
+{ url = "https://github.com/joewa/open-bldc-modelica.git"; rev = "58a83b5b36f267613de4676c95163489b1ddc2e7"; sha256 = "0wf6dn64d2psv9b3xg5227vzpk109r3dqzi4m2wwhrilaxs3v004"; fetchSubmodules = true; }
+]
--- a/pkgs/applications/science/misc/openmodelica/omlibrary/update-src-libs.sh
+++ b/pkgs/applications/science/misc/openmodelica/omlibrary/update-src-libs.sh
@ -0,0 +1,39 @@
+#!/usr/bin/env nix-shell
+#! nix-shell -i bash -p bash
+
+CWD=$PWD
+
+chko() {
+  (
+    T=`mktemp -d`
+    trap "rm -rf $T" EXIT INT PIPE
+    cd $T
+    cat >check.nix <<EOF
+with import <nixpkgs> {};
+fetchgit `cat $CWD/../mkderivation/src-main.nix`
+EOF
+    nix-build check.nix
+    cat result/libraries/Makefile.libs
+  )
+}
+
+getsha256() {
+  URL=$(echo "$1" | sed 's/^"\(.*\)"$/\1/')
+  REV=$(echo "$2" | sed 's/^"\(.*\)"$/\1/')
+  SHA=$(nix run nixpkgs.nix-prefetch-git -c nix-prefetch-git --fetch-submodules "$URL" "$REV" 2>/dev/null | sed -n 's/.*"sha256": "\(.*\)",/\1/g p')
+  echo "{ url = $1; rev = $2; sha256 = \"$SHA\"; fetchSubmodules = true; }"
+}
+
+OUT=src-libs.nix
+
+echo '[' > $OUT
+
+chko |
+grep checkout-git.sh |
+tr \' \" |
+while read NM TGT URL BR REV ; do
+  echo Trying $TGT $URL $REV >&2
+  getsha256 $URL $REV >> $OUT || exit 1
+done
+
+echo ']' >> $OUT
--- a/pkgs/applications/science/misc/openmodelica/omparser/Makefile.in.patch
+++ b/pkgs/applications/science/misc/openmodelica/omparser/Makefile.in.patch
@ -0,0 +1,22 @@
+--- a/Makefile.in
+++ b/Makefile.in
+@@ -23,7 +23,7 @@
+ omedit-testsuite: omedit-testsuite.skip
+ omedit-testsuite.skip: omedit.skip testsuite-depends
+ 	$(MAKE) -f $(defaultMakefileTarget) -C OMEdit/Testsuite
+-omparser: omparser.skip
+omparser: build-dirs omparser.skip
+ omparser.skip:
+ 	test -f $@ || $(MAKE) -C OMParser OMBUILDDIR=@OMBUILDDIR@ "host_short=@host_short@" CC="@CC@" CXX="@CXX@" CFLAGS="@CFLAGS@" CPPFLAGS="@CPPFLAGS@" CXXFLAGS="@CXXFLAGS@"
+ omsimulator: omsimulator.skip
+@@ -134,6 +134,10 @@
+ INSTALL_JAVADIR    = ${DESTDIR}${datadir}/omc/java
+ INSTALL_LOCALEDIR  = ${DESTDIR}${datadir}/locale
+ 
+build-dirs:
+	mkdir -p "@OMBUILDDIR@"/lib/@host_short@/omc
+	mkdir -p "@OMBUILDDIR@"/include/omc
+
+ install-dirs:
+ 	@test ! "${DESTDIR}/@prefix@" -ef "@OMBUILDDIR@" || (echo Error: Install and build dirs are the same && false)
+ 	if [ "@APP@" = ".app" ]; then mkdir -p ${INSTALL_APPDIR}; fi
--- a/pkgs/applications/science/misc/openmodelica/omparser/default.nix
+++ b/pkgs/applications/science/misc/openmodelica/omparser/default.nix
@ -0,0 +1,28 @@
+{ lib
+, pkg-config
+, jre8
+, libuuid
+, openmodelica
+, mkOpenModelicaDerivation
+}:
+
+mkOpenModelicaDerivation rec {
+  pname = "omparser";
+  omdir = "OMParser";
+  omdeps = [ openmodelica.omcompiler ];
+
+  nativeBuildInputs = [ pkg-config ];
+
+  buildInputs = [ jre8 libuuid ];
+
+  patches = [ ./Makefile.in.patch ];
+
+  meta = with lib; {
+    description = "An antlr4-based parser of Modelica files from OpenModelica
+suite";
+    homepage = "https://openmodelica.org";
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [ balodja smironov ];
+    platforms = platforms.linux;
+  };
+}
--- a/pkgs/applications/science/misc/openmodelica/omplot/default.nix
+++ b/pkgs/applications/science/misc/openmodelica/omplot/default.nix
@ -0,0 +1,34 @@
+{ lib
+, qtbase
+, qttools
+, qmake
+, wrapQtAppsHook
+, openmodelica
+, mkOpenModelicaDerivation
+}:
+
+mkOpenModelicaDerivation rec {
+  pname = "omplot";
+  omdir = "OMPlot";
+  omdeps = [ openmodelica.omcompiler ];
+  omautoconf = true;
+
+  nativeBuildInputs = [ qtbase qttools qmake wrapQtAppsHook ];
+
+  postPatch = ''
+    sed -i OMPlot/Makefile.in -e 's|bindir = @includedir@|includedir = @includedir@|'
+    sed -i OMPlot/OMPlot/OMPlotGUI/*.pro -e '/INCLUDEPATH +=/s|$| ../../qwt/src|'
+    sed -i ''$(find -name qmake.m4) -e '/^\s*LRELEASE=/ s|LRELEASE=.*$|LRELEASE=${lib.getDev qttools}/bin/lrelease|'
+  '';
+
+  dontUseQmakeConfigure = true;
+  QMAKESPEC = "linux-clang";
+
+  meta = with lib; {
+    description = "Plotting tool for OpenModelica-generated results files";
+    homepage = "https://openmodelica.org";
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [ balodja smironov ];
+    platforms = platforms.linux;
+  };
+}
--- a/pkgs/applications/science/misc/openmodelica/omshell/default.nix
+++ b/pkgs/applications/science/misc/openmodelica/omshell/default.nix
@ -0,0 +1,40 @@
+{ lib, qttools, qmake, qtwebkit, wrapQtAppsHook, readline, openmodelica, mkOpenModelicaDerivation }:
+
+mkOpenModelicaDerivation rec {
+  pname = "omshell";
+  omdir = "OMShell";
+  omdeps = [ openmodelica.omcompiler ];
+  omautoconf = true;
+
+  nativeBuildInputs = [ qmake wrapQtAppsHook ];
+
+  buildInputs = [ readline qtwebkit ];
+
+  postPatch = with openmodelica; ''
+    sed -i ''$(find -name qmake.m4) -e '/^\s*LRELEASE=/ s|LRELEASE=.*$|LRELEASE=${lib.getDev qttools}/bin/lrelease|'
+    sed -i OMShell/OMShell/OMShellGUI/*.pro -e '
+      s|\$\$\[QT_INSTALL_BINS\]/lrelease|${lib.getDev qttools}/bin/lrelease|
+      /^\s*OMCLIBS =/ s|\$\$(OMBUILDDIR)|${omcompiler}|
+      /^\s*OMCINC =/ s|\$\$(OMBUILDDIR)|${omcompiler}|
+    '
+    sed -i OMShell/OMShell/OMShellGUI/OMShell.config.in -e '
+      s|@OMBUILDDIR@|${omcompiler}|
+      s|@OPENMODELICAHOME@|${omcompiler}|
+    '
+    sed -i OMShell/mosh/src/Makefile.in -e '
+      /^CFLAGS =/ s|-I../../../build|-I${omcompiler}|
+      /^LIBS =/ s|-L@OMBUILDDIR@|-L${omcompiler}|
+      '
+  '';
+
+  dontUseQmakeConfigure = true;
+  QMAKESPEC = "linux-clang";
+
+  meta = with lib; {
+    description = "Interactive OpenModelica session shell";
+    homepage = "https://openmodelica.org";
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [ balodja smironov ];
+    platforms = platforms.linux;
+  };
+}
--- a/pkgs/applications/science/misc/openmodelica/omsimulator/default.nix
+++ b/pkgs/applications/science/misc/openmodelica/omsimulator/default.nix
@ -0,0 +1,26 @@
+{ lib
+, pkg-config
+, boost
+, readline
+, libxml2
+, openmodelica
+, mkOpenModelicaDerivation
+}:
+
+mkOpenModelicaDerivation rec {
+  pname = "omsimulator";
+  omdir = "OMSimulator";
+  omdeps = [ openmodelica.omcompiler ];
+
+  nativeBuildInputs = [ pkg-config ];
+
+  buildInputs = [ readline libxml2 boost ];
+
+  meta = with lib; {
+    description = "The OpenModelica FMI & SSP-based co-simulation environment";
+    homepage = "https://openmodelica.org";
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [ balodja smironov ];
+    platforms = platforms.linux;
+  };
+}
--- a/pkgs/applications/science/misc/openmvg/default.nix
+++ b/pkgs/applications/science/misc/openmvg/default.nix
@ -0,0 +1,50 @@
+{ lib, stdenv, fetchFromGitHub, pkg-config, cmake
+, libjpeg ? null
+, zlib ? null
+, libpng ? null
+, eigen ? null
+, libtiff ? null
+, enableExamples ? false
+, enableDocs ? false }:
+
+stdenv.mkDerivation rec {
+  version = "2.0";
+  pname = "openmvg";
+
+  src = fetchFromGitHub {
+    owner = "openmvg";
+    repo = "openmvg";
+    rev = "v${version}";
+    sha256 = "sha256-6F/xUgZpqY+v6CpwTBhIXI4JdT8HVB0P5JzOL66AVd8=";
+    fetchSubmodules = true;
+  };
+
+  buildInputs = [ libjpeg zlib libpng eigen libtiff ];
+
+  nativeBuildInputs = [ cmake pkg-config ];
+
+  cmakeFlags = [
+    "-DCMAKE_CXX_FLAGS=-std=c++11"
+    "-DOpenMVG_BUILD_EXAMPLES=${if enableExamples then "ON" else "OFF"}"
+    "-DOpenMVG_BUILD_DOC=${if enableDocs then "ON" else "OFF"}"
+  ];
+
+  cmakeDir = "./src";
+
+  dontUseCmakeBuildDir = true;
+
+  # This can be enabled, but it will exhause virtual memory on most machines.
+  enableParallelBuilding = false;
+
+  # Without hardeningDisable, certain flags are passed to the compile that break the build (primarily string format errors)
+  hardeningDisable = [ "all" ];
+
+  meta = {
+    broken = (stdenv.isLinux && stdenv.isAarch64);
+    description = "A library for computer-vision scientists and targeted for the Multiple View Geometry community";
+    homepage = "https://openmvg.readthedocs.io/en/latest/";
+    license = lib.licenses.mpl20;
+    platforms = lib.platforms.linux;
+    maintainers = with lib.maintainers; [ mdaiter ];
+  };
+}
--- a/pkgs/applications/science/misc/rink/default.nix
+++ b/pkgs/applications/science/misc/rink/default.nix
@ -0,0 +1,30 @@
+{ lib, stdenv, fetchFromGitHub, rustPlatform, openssl, pkg-config, ncurses
+, libiconv, Security }:
+
+rustPlatform.buildRustPackage rec {
+  version = "0.6.3";
+  pname = "rink";
+
+  src = fetchFromGitHub {
+    owner = "tiffany352";
+    repo = "rink-rs";
+    rev = "v${version}";
+    sha256 = "sha256-AhC3c6CpV0tlD6d/hFWt7hGj2UsXsOCeujkRSDlpvCM=";
+  };
+
+  cargoSha256 = "sha256-Xo5iYwL4Db+GWMl5UXbPmj0Y0PJYR4Q0aUGnYCd+NB8=";
+
+  nativeBuildInputs = [ pkg-config ];
+  buildInputs = [ ncurses ]
+    ++ (if stdenv.isDarwin then [ libiconv Security ] else [ openssl ]);
+
+  # Some tests fail and/or attempt to use internet servers.
+  doCheck = false;
+
+  meta = with lib; {
+    description = "Unit-aware calculator";
+    homepage = "https://rinkcalc.app";
+    license = with licenses; [ mpl20 gpl3Plus ];
+    maintainers = with maintainers; [ sb0 Br1ght0ne ];
+  };
+}
--- a/pkgs/applications/science/misc/root/5.nix
+++ b/pkgs/applications/science/misc/root/5.nix
@ -0,0 +1,149 @@
+{ lib
+, stdenv
+, fetchurl
+, fetchpatch
+, cmake
+, pcre
+, pkg-config
+, python2
+, libX11
+, libXpm
+, libXft
+, libXext
+, libGLU
+, libGL
+, zlib
+, libxml2
+, lz4
+, xz
+, gsl_1
+, xxHash
+, Cocoa
+, OpenGL
+, noSplash ? false
+}:
+
+stdenv.mkDerivation rec {
+  pname = "root";
+  version = "5.34.38";
+
+  src = fetchurl {
+    url = "https://root.cern.ch/download/root_v${version}.source.tar.gz";
+    sha256 = "1ln448lszw4d6jmbdphkr2plwxxlhmjkla48vmmq750xc1lxlfrc";
+  };
+
+  nativeBuildInputs = [ cmake pkg-config ];
+  buildInputs = [ pcre python2 zlib libxml2 lz4 xz gsl_1 xxHash ]
+    ++ lib.optionals (!stdenv.isDarwin) [ libX11 libXpm libXft libXext libGLU libGL ]
+    ++ lib.optionals (stdenv.isDarwin) [ Cocoa OpenGL ]
+  ;
+
+  patches = [
+    ./sw_vers_root5.patch
+
+    # prevents rootcint from looking in /usr/includes and such
+    ./purify_include_paths_root5.patch
+
+    # disable dictionary generation for stuff that includes libc headers
+    # our glibc requires a modern compiler
+    ./disable_libc_dicts_root5.patch
+
+    (fetchpatch {
+      name = "root5-gcc9-fix.patch";
+      url = "https://github.com/root-project/root/commit/348f30a6a3b5905ef734a7bd318bc0ee8bca6dc9.diff";
+      sha256 = "0dvrsrkpacyn5z87374swpy7aciv9a8s6m61b4iqd7a956r67rn3";
+    })
+    (fetchpatch {
+      name = "root5-gcc10-fix.patch";
+      url = "https://github.com/root-project/root/commit/3c243b18768d3c3501faf3ca4e4acfc071021350.diff";
+      sha256 = "1hjmgnp4zx6im8ps78673x0rrhmfyy1nffhgxjlfl1r2z8cq210z";
+    })
+  ];
+
+  preConfigure = ''
+    # binutils 2.37 fixes
+    fixupList=(
+      cint/demo/gl/make0
+      cint/demo/exception/Makefile
+      cint/demo/makecint/KRcc/Makefile
+      cint/demo/makecint/Stub2/Make2
+      cint/demo/makecint/Array/Makefile
+      cint/demo/makecint/DArray/Makefile
+      cint/demo/makecint/ReadFile/Makefile
+      cint/demo/makecint/stl/Makefile
+      cint/demo/makecint/Stub2/Make1
+      cint/cint/include/makemat
+      cint/cint/lib/WildCard/Makefile
+      cint/cint/include/make.arc
+      cint/cint/lib/qt/Makefile
+      cint/cint/lib/pthread/Makefile
+      graf2d/asimage/src/libAfterImage/Makefile.in
+    )
+    for toFix in "''${fixupList[@]}"; do
+      substituteInPlace "$toFix" --replace "clq" "cq"
+    done
+
+    patchShebangs build/unix/
+    ln -s ${lib.getDev stdenv.cc.libc}/include/AvailabilityMacros.h cint/cint/include/
+
+    # __malloc_hook is deprecated
+    substituteInPlace misc/memstat/src/TMemStatHook.cxx \
+      --replace "defined(R__GNU) && (defined(R__LINUX) || defined(__APPLE__))" \
+                "defined(R__GNU) && (defined(__APPLE__))"
+  ''
+  # Fix CINTSYSDIR for "build" version of rootcint
+  # This is probably a bug that breaks out-of-source builds
+  + ''
+    substituteInPlace cint/cint/src/loadfile.cxx\
+      --replace 'env = "cint";' 'env = "'`pwd`'/cint";'
+  '' + lib.optionalString noSplash ''
+    substituteInPlace rootx/src/rootx.cxx --replace "gNoLogo = false" "gNoLogo = true"
+  '';
+
+  cmakeFlags = [
+    "-Drpath=ON"
+    "-DCMAKE_INSTALL_LIBDIR=lib"
+    "-DCMAKE_INSTALL_INCLUDEDIR=include"
+    "-DCMAKE_CXX_FLAGS=-std=c++11"
+    "-Dalien=OFF"
+    "-Dbonjour=OFF"
+    "-Dcastor=OFF"
+    "-Dchirp=OFF"
+    "-Ddavix=OFF"
+    "-Ddcache=OFF"
+    "-Dfftw3=OFF"
+    "-Dfitsio=OFF"
+    "-Dfortran=OFF"
+    "-Dgfal=OFF"
+    "-Dgsl_shared=ON"
+    "-Dgviz=OFF"
+    "-Dhdfs=OFF"
+    "-Dkrb5=OFF"
+    "-Dldap=OFF"
+    "-Dmathmore=ON"
+    "-Dmonalisa=OFF"
+    "-Dmysql=OFF"
+    "-Dodbc=OFF"
+    "-Dopengl=ON"
+    "-Doracle=OFF"
+    "-Dpgsql=OFF"
+    "-Dpythia6=OFF"
+    "-Dpythia8=OFF"
+    "-Drfio=OFF"
+    "-Dsqlite=OFF"
+    "-Dssl=OFF"
+    "-Dxml=ON"
+    "-Dxrootd=OFF"
+  ]
+  ++ lib.optional stdenv.isDarwin "-DOPENGL_INCLUDE_DIR=${OpenGL}/Library/Frameworks";
+
+  setupHook = ./setup-hook.sh;
+
+  meta = with lib; {
+    homepage = "https://root.cern.ch/";
+    description = "A data analysis framework";
+    platforms = platforms.unix;
+    maintainers = with maintainers; [ veprbl ];
+    license = licenses.lgpl21;
+  };
+}
--- a/pkgs/applications/science/misc/root/default.nix
+++ b/pkgs/applications/science/misc/root/default.nix
@ -0,0 +1,192 @@
+{ stdenv
+, lib
+, fetchurl
+, fetchpatch
+, makeWrapper
+, cmake
+, git
+, ftgl
+, gl2ps
+, glew
+, gsl
+, lapack
+, libX11
+, libXpm
+, libXft
+, libXext
+, libGLU
+, libGL
+, libxml2
+, llvm_9
+, lz4
+, xz
+, openblas
+, pcre
+, nlohmann_json
+, pkg-config
+, python
+, xxHash
+, zlib
+, zstd
+, libAfterImage
+, giflib
+, libjpeg
+, libtiff
+, libpng
+, tbb
+, Cocoa
+, CoreSymbolication
+, OpenGL
+, noSplash ? false
+}:
+
+stdenv.mkDerivation rec {
+  pname = "root";
+  version = "6.24.06";
+
+  src = fetchurl {
+    url = "https://root.cern.ch/download/root_v${version}.source.tar.gz";
+    sha256 = "sha256-kH9p9LrKHk8w7rSXlZjKdZm2qoA8oEboDiW2u6oO9SI=";
+  };
+
+  nativeBuildInputs = [ makeWrapper cmake pkg-config git ];
+  buildInputs = [
+    ftgl
+    gl2ps
+    glew
+    pcre
+    zlib
+    zstd
+    lapack
+    libxml2
+    llvm_9
+    lz4
+    xz
+    gsl
+    openblas
+    xxHash
+    libAfterImage
+    giflib
+    libjpeg
+    libtiff
+    libpng
+    nlohmann_json
+    python.pkgs.numpy
+    tbb
+  ]
+  ++ lib.optionals (!stdenv.isDarwin) [ libX11 libXpm libXft libXext libGLU libGL ]
+  ++ lib.optionals (stdenv.isDarwin) [ Cocoa CoreSymbolication OpenGL ]
+  ;
+
+  patches = [
+    ./sw_vers.patch
+
+    # Fix builtin_llvm=OFF support
+    (fetchpatch {
+      url = "https://github.com/root-project/root/commit/0cddef5d3562a89fe254e0036bb7d5ca8a5d34d2.diff";
+      excludes = [ "interpreter/cling/tools/plugins/clad/CMakeLists.txt" ];
+      sha256 = "sha256-VxWUbxRHB3O6tERFQdbGI7ypDAZD3sjSi+PYfu1OAbM=";
+    })
+  ];
+
+  # Fix build against vanilla LLVM 9
+  postPatch = ''
+    sed \
+      -e '/#include "llvm.*RTDyldObjectLinkingLayer.h"/i#define private protected' \
+      -e '/#include "llvm.*RTDyldObjectLinkingLayer.h"/a#undef private' \
+      -i interpreter/cling/lib/Interpreter/IncrementalJIT.h
+  '';
+
+  preConfigure = ''
+    rm -rf builtins/*
+    substituteInPlace cmake/modules/SearchInstalledSoftware.cmake \
+      --replace 'set(lcgpackages ' '#set(lcgpackages '
+
+    # Don't require textutil on macOS
+    : > cmake/modules/RootCPack.cmake
+
+    # Hardcode path to fix use with cmake
+    sed -i cmake/scripts/ROOTConfig.cmake.in \
+      -e '1iset(nlohmann_json_DIR "${nlohmann_json}/lib/cmake/nlohmann_json/")'
+
+    patchShebangs build/unix/
+  '' + lib.optionalString noSplash ''
+    substituteInPlace rootx/src/rootx.cxx --replace "gNoLogo = false" "gNoLogo = true"
+  '' + lib.optionalString stdenv.isDarwin ''
+    # Eliminate impure reference to /System/Library/PrivateFrameworks
+    substituteInPlace core/CMakeLists.txt \
+      --replace "-F/System/Library/PrivateFrameworks" ""
+  '';
+
+  cmakeFlags = [
+    "-Drpath=ON"
+    "-DCMAKE_INSTALL_BINDIR=bin"
+    "-DCMAKE_INSTALL_LIBDIR=lib"
+    "-DCMAKE_INSTALL_INCLUDEDIR=include"
+    "-Dbuiltin_llvm=OFF"
+    "-Dbuiltin_nlohmannjson=OFF"
+    "-Dbuiltin_openui5=OFF"
+    "-Dalien=OFF"
+    "-Dbonjour=OFF"
+    "-Dcastor=OFF"
+    "-Dchirp=OFF"
+    "-Dclad=OFF"
+    "-Ddavix=OFF"
+    "-Ddcache=OFF"
+    "-Dfail-on-missing=ON"
+    "-Dfftw3=OFF"
+    "-Dfitsio=OFF"
+    "-Dfortran=OFF"
+    "-Dimt=ON"
+    "-Dgfal=OFF"
+    "-Dgviz=OFF"
+    "-Dhdfs=OFF"
+    "-Dhttp=ON"
+    "-Dkrb5=OFF"
+    "-Dldap=OFF"
+    "-Dmonalisa=OFF"
+    "-Dmysql=OFF"
+    "-Dodbc=OFF"
+    "-Dopengl=ON"
+    "-Doracle=OFF"
+    "-Dpgsql=OFF"
+    "-Dpythia6=OFF"
+    "-Dpythia8=OFF"
+    "-Drfio=OFF"
+    "-Droot7=OFF"
+    "-Dsqlite=OFF"
+    "-Dssl=OFF"
+    "-Dtmva=ON"
+    "-Dvdt=OFF"
+    "-Dwebgui=OFF"
+    "-Dxml=ON"
+    "-Dxrootd=OFF"
+  ]
+  ++ lib.optional (stdenv.cc.libc != null) "-DC_INCLUDE_DIRS=${lib.getDev stdenv.cc.libc}/include"
+  ++ lib.optionals stdenv.isDarwin [
+    "-DOPENGL_INCLUDE_DIR=${OpenGL}/Library/Frameworks"
+    "-DCMAKE_DISABLE_FIND_PACKAGE_Python2=TRUE"
+
+    # fatal error: module map file '/nix/store/<hash>-Libsystem-osx-10.12.6/include/module.modulemap' not found
+    # fatal error: could not build module '_Builtin_intrinsics'
+    "-Druntime_cxxmodules=OFF"
+  ];
+
+  postInstall = ''
+    for prog in rootbrowse rootcp rooteventselector rootls rootmkdir rootmv rootprint rootrm rootslimtree; do
+      wrapProgram "$out/bin/$prog" \
+        --set PYTHONPATH "$out/lib" \
+        --set ${lib.optionalString stdenv.isDarwin "DY"}LD_LIBRARY_PATH "$out/lib"
+    done
+  '';
+
+  setupHook = ./setup-hook.sh;
+
+  meta = with lib; {
+    homepage = "https://root.cern.ch/";
+    description = "A data analysis framework";
+    platforms = platforms.unix;
+    maintainers = [ maintainers.veprbl ];
+    license = licenses.lgpl21;
+  };
+}
--- a/pkgs/applications/science/misc/root/disable_libc_dicts_root5.patch
+++ b/pkgs/applications/science/misc/root/disable_libc_dicts_root5.patch
@ -0,0 +1,27 @@
+diff --git a/cint/ROOT/CMakeLists.txt b/cint/ROOT/CMakeLists.txt
+--- a/cint/ROOT/CMakeLists.txt
+++ b/cint/ROOT/CMakeLists.txt
+@@ -47,21 +47,13 @@ set(CINTSTLDLLHEADERS
+     ${CMAKE_SOURCE_DIR}/cint/cint/lib/stdstrct/stdcxxfunc.h
+   )
+ set(CINTINCDLLNAMES 
+-    stdfunc 
+#    stdfunc 
+ #    stdcxxfunc
+    )
+ set(CINTINCDLLHEADERS
+-    ${CMAKE_SOURCE_DIR}/cint/cint/lib/stdstrct/stdfunc.h 
+#    ${CMAKE_SOURCE_DIR}/cint/cint/lib/stdstrct/stdfunc.h 
+ #    ${CMAKE_SOURCE_DIR}/cint/cint/lib/stdstrct/stdcxxfunc.h
+    )
+-if(NOT WIN32)
+-  set(CINTSTLDLLNAMES ${CINTSTLDLLNAMES}  valarray)
+-  set(CINTSTLDLLHEADERS ${CINTSTLDLLHEADERS} ${CINTDLLDIR}/vary.h)
+-  set(CINTINCDLLNAMES ${CINTINCDLLNAMES} posix ipc)
+-  set(CINTINCDLLHEADERS ${CINTINCDLLHEADERS} 
+-    ${CMAKE_SOURCE_DIR}/cint/cint/lib/posix/exten.h 
+-    ${CMAKE_SOURCE_DIR}/cint/cint/lib/ipc/ipcif.h)
+-endif()
+ 
+ set(CINTBUILDLOADER
+     vector 
--- a/pkgs/applications/science/misc/root/purify_include_paths_root5.patch
+++ b/pkgs/applications/science/misc/root/purify_include_paths_root5.patch
@ -0,0 +1,204 @@
+diff --git a/cint/cint/src/loadfile.cxx b/cint/cint/src/loadfile.cxx
+--- a/cint/cint/src/loadfile.cxx
+++ b/cint/cint/src/loadfile.cxx
+@@ -1365,92 +1365,6 @@ int G__statfilename(const char *filenamein, struct stat *statBuf,
+          }
+       }         
+ #endif /* G__EDU_VERSION */
+-      
+-#ifdef G__VISUAL
+-      /**********************************************
+-       * try /msdev/include
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         workname.Format("/msdev/include/%s%s",filename(),addpost[i2]);
+-         res = stat( workname, statBuf );         
+-         if (res==0) {
+-            if (fullPath) fullPath->Swap(workname);
+-            return res;
+-         }
+-      }
+-#endif /* G__VISUAL */
+-         
+-#ifdef G__SYMANTEC
+-      /**********************************************
+-       * try /sc/include
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         workname.Format("/sc/include/%s%s",filename(),addpost[i2]);
+-         res = stat( workname, statBuf );         
+-         if (res==0) {
+-            if (fullPath) fullPath->Swap(workname);
+-            return res;
+-         }
+-      }
+-#endif // G__SYMANTEC
+-         
+-#ifndef G__WIN32
+-      /**********************************************
+-       * try /usr/include/filename
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         workname.Format("/usr/include/%s%s",filename(),addpost[i2]);
+-         res = stat( workname, statBuf );         
+-         if (res==0) {
+-            if (fullPath) fullPath->Swap(workname);
+-            return res;
+-         }
+-      }
+-#endif
+-      
+-#ifdef __GNUC__
+-      /**********************************************
+-       * try /usr/include/g++/filename
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         workname.Format("/usr/include/g++/%s%s",filename(),addpost[i2]);
+-         res = stat( workname, statBuf );         
+-         if (res==0) {
+-            if (fullPath) fullPath->Swap(workname);
+-            return res;
+-         }
+-      }
+-#endif /* __GNUC__ */
+-      
+-#ifndef G__WIN32
+-      /* #ifdef __hpux */
+-      /**********************************************
+-       * try /usr/include/CC/filename
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         workname.Format("/usr/include/CC/%s%s",filename(),addpost[i2]);
+-         res = stat( workname, statBuf );         
+-         if (res==0) {
+-            if (fullPath) fullPath->Swap(workname);
+-            return res;
+-         }
+-      }         
+-#endif
+-         
+-#ifndef G__WIN32
+-      /**********************************************
+-       * try /usr/include/codelibs/filename
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         workname.Format("/usr/include/codelibs/%s%s"
+-                         ,filename(),addpost[i2]);
+-         res = stat( workname, statBuf );         
+-         if (res==0) {
+-            if (fullPath) fullPath->Swap(workname);
+-            return res;
+-         }
+-      }
+-#endif
+    }
+    return -1;
+ }
+@@ -1960,107 +1874,6 @@ int G__loadfile(const char *filenamein)
+       }
+       if(G__ifile.fp) break;
+ #endif /* G__EDU_VERSION */
+-
+-#ifdef G__VISUAL
+-      /**********************************************
+-       * try /msdev/include
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         G__snprintf(G__ifile.name,G__MAXFILENAME,"/msdev/include/%s%s",filename(),addpost[i2]);
+-#ifndef G__WIN32
+-        G__ifile.fp = fopen(G__ifile.name,"r");
+-#else
+-        G__ifile.fp = fopen(G__ifile.name,"rb");
+-#endif
+-        G__globalcomp=G__store_globalcomp;
+-      }
+-      if(G__ifile.fp) break;
+-#endif /* G__VISUAL */
+-
+-#ifdef G__SYMANTEC
+-      /**********************************************
+-       * try /sc/include
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         G__snprintf(G__ifile.name,G__MAXFILENAME,"/sc/include/%s%s",filename(),addpost[i2]);
+-#ifndef G__WIN32
+-        G__ifile.fp = fopen(G__ifile.name,"r");
+-#else
+-        G__ifile.fp = fopen(G__ifile.name,"rb");
+-#endif
+-        G__globalcomp=G__store_globalcomp;
+-      }
+-      if(G__ifile.fp) break;
+-#endif /* G__SYMANTEC */
+-
+-#ifndef G__WIN32
+-      /**********************************************
+-       * try /usr/include/filename
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         G__snprintf(G__ifile.name,G__MAXFILENAME,"/usr/include/%s%s",filename(),addpost[i2]);
+-#ifndef G__WIN32
+-        G__ifile.fp = fopen(G__ifile.name,"r");
+-#else
+-        G__ifile.fp = fopen(G__ifile.name,"rb");
+-#endif
+-        G__globalcomp=G__store_globalcomp;
+-      }
+-      if(G__ifile.fp) break;
+-#endif
+-
+-#ifdef __GNUC__
+-      /**********************************************
+-       * try /usr/include/g++/filename
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         G__snprintf(G__ifile.name,G__MAXFILENAME,"/usr/include/g++/%s%s",filename(),addpost[i2]);
+-#ifndef G__WIN32
+-        G__ifile.fp = fopen(G__ifile.name,"r");
+-#else
+-        G__ifile.fp = fopen(G__ifile.name,"rb");
+-#endif
+-        G__globalcomp=G__store_globalcomp;
+-      }
+-      if(G__ifile.fp) break;
+-#endif /* __GNUC__ */
+-
+-#ifndef G__WIN32
+-/* #ifdef __hpux */
+-      /**********************************************
+-       * try /usr/include/CC/filename
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         G__snprintf(G__ifile.name,G__MAXFILENAME,"/usr/include/CC/%s%s",filename(),addpost[i2]);
+-#ifndef G__WIN32
+-        G__ifile.fp = fopen(G__ifile.name,"r");
+-#else
+-        G__ifile.fp = fopen(G__ifile.name,"rb");
+-#endif
+-        G__globalcomp=G__store_globalcomp;
+-      }
+-      if(G__ifile.fp) break;
+-/* #endif __hpux */
+-#endif
+-
+-#ifndef G__WIN32
+-/* #ifdef __hpux */
+-      /**********************************************
+-       * try /usr/include/codelibs/filename
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-        G__snprintf(G__ifile.name,G__MAXFILENAME,"/usr/include/codelibs/%s%s"
+-                    ,filename(),addpost[i2]);
+-#ifndef G__WIN32
+-        G__ifile.fp = fopen(G__ifile.name,"r");
+-#else
+-        G__ifile.fp = fopen(G__ifile.name,"rb");
+-#endif
+-        G__globalcomp=G__store_globalcomp;
+-      }
+-      if(G__ifile.fp) break;
+-/* #endif __hpux */
+-#endif
+     }
+   }
+ 
--- a/pkgs/applications/science/misc/root/setup-hook.sh
+++ b/pkgs/applications/science/misc/root/setup-hook.sh
@ -0,0 +1,13 @@
+thisroot () {
+    # Workaround thisroot.sh dependency on man
+    if [ -z "${MANPATH-}" ]; then
+        MANPATH=:
+    fi
+    local oldOpts="-u"
+    shopt -qo nounset || oldOpts="+u"
+    set +u
+    source @out@/bin/thisroot.sh
+    set "$oldOpts"
+}
+
+postHooks+=(thisroot)
--- a/pkgs/applications/science/misc/root/sw_vers.patch
+++ b/pkgs/applications/science/misc/root/sw_vers.patch
@ -0,0 +1,87 @@
+diff a/cmake/modules/SetUpMacOS.cmake b/cmake/modules/SetUpMacOS.cmake
+--- a/cmake/modules/SetUpMacOS.cmake
+++ b/cmake/modules/SetUpMacOS.cmake
+@@ -28,17 +28,10 @@ if(CMAKE_VERSION VERSION_LESS 3.14.4)
+ endif()
+ 
+ if (CMAKE_SYSTEM_NAME MATCHES Darwin)
+-  EXECUTE_PROCESS(COMMAND sw_vers "-productVersion"
+-                  COMMAND cut -d . -f 1-2
+-                  OUTPUT_VARIABLE MACOSX_VERSION OUTPUT_STRIP_TRAILING_WHITESPACE)
+-
+   MESSAGE(STATUS "Found a macOS system ${MACOSX_VERSION}")
+ 
+-  if(MACOSX_VERSION VERSION_GREATER 10.7 AND ${CMAKE_CXX_COMPILER_ID} MATCHES Clang)
+     set(libcxx ON CACHE BOOL "Build using libc++" FORCE)
+-  endif()
+ 
+-  if(MACOSX_VERSION VERSION_GREATER 10.4)
+     #TODO: check haveconfig and rpath -> set rpath true
+     #TODO: check Thread, define link command
+     #TODO: more stuff check configure script
+@@ -57,22 +50,7 @@ if (CMAKE_SYSTEM_NAME MATCHES Darwin)
+        SET(CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS "${CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS} -m64")
+        SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64")
+        SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -m64")
+-    else()
+-       SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m32")
+-       SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -m32")
+-       SET(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -m32")
+     endif()
+-  endif()
+-
+-  if(MACOSX_VERSION VERSION_GREATER 10.6)
+-    set(MACOSX_SSL_DEPRECATED ON)
+-  endif()
+-  if(MACOSX_VERSION VERSION_GREATER 10.7)
+-    set(MACOSX_ODBC_DEPRECATED ON)
+-  endif()
+-  if(MACOSX_VERSION VERSION_GREATER 10.8)
+-    set(MACOSX_GLU_DEPRECATED ON)
+-  endif()
+ 
+   if (CMAKE_COMPILER_IS_GNUCXX)
+      SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pipe -W -Wshadow -Wall -Woverloaded-virtual -fsigned-char -fno-common")
+@@ -130,7 +108,6 @@ if (CMAKE_SYSTEM_NAME MATCHES Darwin)
+   endif()
+ 
+   #---Set Linker flags----------------------------------------------------------------------
+-  set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -mmacosx-version-min=${MACOSX_VERSION}")
+ else (CMAKE_SYSTEM_NAME MATCHES Darwin)
+   MESSAGE(FATAL_ERROR "There is no setup for this this Apple system up to now. Don't know waht to do. Stop cmake at this point.")
+ endif (CMAKE_SYSTEM_NAME MATCHES Darwin)
+diff a/config/root-config.in b/config/root-config.in
+--- a/config/root-config.in
+++ b/config/root-config.in
+@@ -312,12 +312,6 @@ macosxicc)
+    ;;
+ macosx64|macosxarm64)
+    # MacOS X with gcc (GNU cc v4.x) in 64 bit mode
+-   macosx_major=`sw_vers | sed -n 's/ProductVersion://p' | cut -d . -f 1 | sed -e 's/^[[:space:]]*//'`
+-   macosx_minor=`sw_vers | sed -n 's/ProductVersion://p' | cut -d . -f 2`
+-   # cannot find the one linked to libGraf if relocated after built
+-   if [ $macosx_major -eq 10 -a $macosx_minor -le 4 ]; then
+-      rootlibs="$rootlibs -lfreetype"
+-   fi
+    auxcflags="${cxxversionflag} -m64"
+    auxldflags="-m64"
+    auxlibs="-lm -ldl"
+@@ -378,18 +372,11 @@ freebsd* | openbsd* | linux*)
+    done
+    ;;
+ macosx*)
+-   if [ \( $macosx_major -eq 10 -a $macosx_minor -ge 5 \) -o $macosx_major -gt 10  ]; then
+       auxcflags="-pthread $auxcflags"
+       auxlibs="-lpthread $auxlibs"
+-   else
+-      auxcflags="-D_REENTRANT $auxcflags"
+-      auxlibs="-lpthread $auxlibs"
+-   fi
+    for f in $features ; do
+       if test "x$f" = "xrpath" ; then
+-         if [ \( $macosx_major -eq 10 -a $macosx_minor -ge 5 \) -o $macosx_major -gt 10  ]; then
+             auxlibs="-Wl,-rpath,$libdir $auxlibs"
+-         fi
+       fi
+       if test "x$f" = "xlibcxx" ; then
+          auxcflags="-stdlib=libc++ $auxcflags"
--- a/pkgs/applications/science/misc/root/sw_vers_root5.patch
+++ b/pkgs/applications/science/misc/root/sw_vers_root5.patch
@ -0,0 +1,104 @@
+diff --git a/build/unix/compiledata.sh b/build/unix/compiledata.sh
+--- a/build/unix/compiledata.sh
+++ b/build/unix/compiledata.sh
+@@ -49,7 +49,7 @@ fi
+ 
+ if [ "$ARCH" = "macosx" ] || [ "$ARCH" = "macosx64" ] || \
+    [ "$ARCH" = "macosxicc" ]; then
+-   macosx_minor=`sw_vers | sed -n 's/ProductVersion://p' | cut -d . -f 2`
+   macosx_minor=7
+    SOEXT="so"
+    if [ $macosx_minor -ge 5 ]; then
+       if [ "x`echo $SOFLAGS | grep -- '-install_name'`" != "x" ]; then
+diff --git a/cmake/modules/SetUpMacOS.cmake b/cmake/modules/SetUpMacOS.cmake
+--- a/cmake/modules/SetUpMacOS.cmake
+++ b/cmake/modules/SetUpMacOS.cmake
+@@ -12,25 +12,11 @@ set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} /usr/X11R6)
+ #---------------------------------------------------------------------------------------------------------
+ 
+ if (CMAKE_SYSTEM_NAME MATCHES Darwin)
+-  EXECUTE_PROCESS(COMMAND sw_vers "-productVersion"
+-                  COMMAND cut -d . -f 1-2
+-                  OUTPUT_VARIABLE MACOSX_VERSION OUTPUT_STRIP_TRAILING_WHITESPACE)
+-  MESSAGE(STATUS "Found a Mac OS X System ${MACOSX_VERSION}")
+-  EXECUTE_PROCESS(COMMAND sw_vers "-productVersion"
+-                  COMMAND cut -d . -f 2
+-                  OUTPUT_VARIABLE MACOSX_MINOR OUTPUT_STRIP_TRAILING_WHITESPACE)
+-
+-  if(MACOSX_VERSION VERSION_GREATER 10.7 AND ${CMAKE_CXX_COMPILER_ID} STREQUAL Clang)
+     set(libcxx ON CACHE BOOL "Build using libc++" FORCE)
+-  endif()
+ 
+-  if(${MACOSX_MINOR} GREATER 4)
+     #TODO: check haveconfig and rpath -> set rpath true
+     #TODO: check Thread, define link command
+     #TODO: more stuff check configure script
+-    execute_process(COMMAND /usr/sbin/sysctl machdep.cpu.extfeatures OUTPUT_VARIABLE SYSCTL_OUTPUT)
+-    if(${SYSCTL_OUTPUT} MATCHES 64)
+-       MESSAGE(STATUS "Found a 64bit system")
+        set(ROOT_ARCHITECTURE macosx64)
+        SET(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS}")
+        SET(CMAKE_SHARED_LIBRARY_CREATE_C_FLAGS "${CMAKE_SHARED_LIBRARY_CREATE_C_FLAGS} -m64")
+@@ -38,28 +24,6 @@ if (CMAKE_SYSTEM_NAME MATCHES Darwin)
+        SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64")
+        SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -m64")
+        SET(CMAKE_FORTRAN_FLAGS "${CMAKE_FORTRAN_FLAGS} -m64")
+-    else(${SYSCTL_OUTPUT} MATCHES 64)
+-       MESSAGE(STATUS "Found a 32bit system")
+-       SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m32")
+-       SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -m32")
+-       SET(CMAKE_FORTRAN_FLAGS "${CMAKE_FORTRAN_FLAGS} -m32")
+-    endif(${SYSCTL_OUTPUT} MATCHES 64)
+-  endif()
+-
+-  if(MACOSX_VERSION VERSION_GREATER 10.6)
+-    set(MACOSX_SSL_DEPRECATED ON)
+-  endif()
+-  if(MACOSX_VERSION VERSION_GREATER 10.7)
+-    set(MACOSX_ODBC_DEPRECATED ON)
+-  endif()
+-  if(MACOSX_VERSION VERSION_GREATER 10.8)
+-    set(MACOSX_GLU_DEPRECATED ON)
+-    set(MACOSX_KRB5_DEPRECATED ON)
+-    set(MACOSX_TMPNAM_DEPRECATED ON)
+-  endif()
+-  if(MACOSX_VERSION VERSION_GREATER 10.9)
+-    set(MACOSX_LDAP_DEPRECATED ON)
+-  endif()
+ 
+   if (CMAKE_COMPILER_IS_GNUCXX)
+      message(STATUS "Found GNU compiler collection")
+@@ -132,7 +96,7 @@ if (CMAKE_SYSTEM_NAME MATCHES Darwin)
+   endif()
+ 
+   #---Set Linker flags----------------------------------------------------------------------
+-  set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS}  -mmacosx-version-min=${MACOSX_VERSION} -Wl,-rpath,@loader_path/../lib")
+  set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-rpath,@loader_path/../lib")
+ 
+ 
+ else (CMAKE_SYSTEM_NAME MATCHES Darwin)
+diff --git a/config/root-config.in b/config/root-config.in
+--- a/config/root-config.in
+++ b/config/root-config.in
+@@ -391,7 +391,7 @@ macosxicc)
+    ;;
+ macosx64)
+    # MacOS X with gcc (GNU cc v4.x) in 64 bit mode
+-   macosx_minor=`sw_vers | sed -n 's/ProductVersion://p' | cut -d . -f 2`
+   macosx_minor=7
+    # cannot find the one linked to libGraf if relocated after built
+    if [ $macosx_minor -le 4 ]; then
+       rootlibs="$rootlibs -lfreetype"
+diff --git a/cint/ROOT/CMakeLists.txt b/cint/ROOT/CMakeLists.txt
+--- a/cint/ROOT/CMakeLists.txt
+++ b/cint/ROOT/CMakeLists.txt
+@@ -232,9 +232,7 @@ foreach(_name ${CINTINCDLLNAMES})
+                        DEPENDS ${HEADER_OUTPUT_PATH}/systypes.h
+                       )
+
+-    if(MACOSX_MINOR GREATER 4)
+       set(_ExtraFlag "-D__DARWIN_UNIX03")
+-    endif()
+
+     add_custom_command(OUTPUT ${OutFileName}
+                        COMMAND cint_tmp -K -w1 -z${_name} -n${OutFileName} -D__MAKECINT__ -DG__MAKECINT ${_ExtraFlag} -c-2 -Z0 ${InFileName} ${AdditionalHeaderFiles} ${CMAKE_BINARY_DIR}/cint/cint/include/sys/types.h ${CMAKE_SOURCE_DIR}/cint/cint/lib/posix/posix.h
--- a/pkgs/applications/science/misc/sasview/default.nix
+++ b/pkgs/applications/science/misc/sasview/default.nix
@ -0,0 +1,62 @@
+{ lib
+, python3
+, fetchFromGitHub
+, which
+, wrapQtAppsHook
+}:
+
+python3.pkgs.buildPythonApplication rec {
+  pname = "sasview";
+  version = "5.0.4";
+
+  src = fetchFromGitHub {
+    owner = "SasView";
+    repo = "sasview";
+    rev = "v${version}";
+    hash = "sha256-TjcchqA6GCvkr59ZgDuGglan2RxLp+aMjJk28XhvoiY=";
+  };
+
+  nativeBuildInputs = [
+    python3.pkgs.pyqt5
+    wrapQtAppsHook
+  ];
+
+  propagatedBuildInputs = with python3.pkgs; [
+    bumps
+    h5py
+    lxml
+    periodictable
+    pillow
+    pyparsing
+    pyqt5
+    qt5reactor
+    sasmodels
+    scipy
+    setuptools
+    xhtml2pdf
+  ];
+
+  postBuild = ''
+    ${python3.interpreter} src/sas/qtgui/convertUI.py
+  '';
+
+  dontWrapQtApps = true;
+
+  makeWrapperArgs = [
+    "\${qtWrapperArgs[@]}"
+  ];
+
+  checkInputs = with python3.pkgs; [
+    pytestCheckHook
+    unittest-xml-reporting
+  ];
+
+  pytestFlagsArray = [ "test" ];
+
+  meta = with lib; {
+    homepage = "https://www.sasview.org";
+    description = "Fitting and data analysis for small angle scattering data";
+    maintainers = with maintainers; [ rprospero ];
+    license = licenses.bsd3;
+  };
+}
--- a/pkgs/applications/science/misc/sasview/xhtml2pdf.nix
+++ b/pkgs/applications/science/misc/sasview/xhtml2pdf.nix
@ -0,0 +1,33 @@
+{lib, fetchPypi, buildPythonPackage, html5lib, httplib2, nose, pillow, pypdf2, reportlab}:
+
+let
+  #xhtml2pdf specifically requires version "1.0b10" of html5lib
+  html5 = html5lib.overrideAttrs( oldAttrs: rec {
+    name = "${oldAttrs.pname}-${version}";
+    version = "1.0b10";
+    src = oldAttrs.src.override {
+      inherit version;
+      sha256 = "1yd068a5c00wd0ajq0hqimv7fd82lhrw0w3s01vbhy9bbd6xapqd";
+    };
+  });
+in
+
+buildPythonPackage rec {
+  pname = "xhtml2pdf";
+  version = "0.2.1";
+
+  buildInputs = [html5];
+  propagatedBuildInputs = [httplib2 nose pillow pypdf2 reportlab html5];
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1n9r8zdk9gc2x539fq60bhszmd421ipj8g78zmsn3njvma1az9k1";
+  };
+
+  meta = {
+    description = "A pdf converter for the ReportLab Toolkit";
+    homepage = "https://github.com/xhtml2pdf/xhtml2pdf";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ rprospero ];
+  };
+}
--- a/pkgs/applications/science/misc/simgrid/default.nix
+++ b/pkgs/applications/science/misc/simgrid/default.nix
@ -0,0 +1,122 @@
+{ stdenv, lib, fetchFromGitLab, cmake, perl, python3, boost
+, fortranSupport ? false, gfortran
+, buildDocumentation ? false, fig2dev, ghostscript, doxygen
+, buildJavaBindings ? false, openjdk
+, buildPythonBindings ? true, python3Packages
+, modelCheckingSupport ? false, libunwind, libevent, elfutils # Inside elfutils: libelf and libdw
+, bmfSupport ? true, eigen
+, minimalBindings ? false
+, debug ? false
+, optimize ? (!debug)
+, moreTests ? false
+, withoutBin ? false
+}:
+
+with lib;
+
+let
+  optionOnOff = option: if option then "on" else "off";
+in
+
+stdenv.mkDerivation rec {
+  pname = "simgrid";
+  version = "3.31";
+
+  src = fetchFromGitLab {
+    domain = "framagit.org";
+    owner = pname;
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "sha256-K6YkkCMxc2lqxHIwyuLiwcp3m49sqbEtOlwZh4L1YJg=";
+  };
+
+  propagatedBuildInputs = [ boost ];
+  nativeBuildInputs = [ cmake perl python3 ]
+    ++ optionals fortranSupport [ gfortran ]
+    ++ optionals buildJavaBindings [ openjdk ]
+    ++ optionals buildPythonBindings [ python3Packages.pybind11 ]
+    ++ optionals buildDocumentation [ fig2dev ghostscript doxygen ]
+    ++ optionals bmfSupport [ eigen ]
+    ++ optionals modelCheckingSupport [ libunwind libevent elfutils ];
+
+  outputs = [ "out" ]
+    ++ optionals buildPythonBindings [ "python" ];
+
+  # "Release" does not work. non-debug mode is Debug compiled with optimization
+  cmakeBuildType = "Debug";
+  cmakeFlags = [
+    "-Denable_documentation=${optionOnOff buildDocumentation}"
+    "-Denable_java=${optionOnOff buildJavaBindings}"
+    "-Denable_python=${optionOnOff buildPythonBindings}"
+    "-DSIMGRID_PYTHON_LIBDIR=./" # prevents CMake to install in ${python3} dir
+    "-Denable_msg=${optionOnOff buildJavaBindings}"
+    "-Denable_fortran=${optionOnOff fortranSupport}"
+    "-Denable_model-checking=${optionOnOff modelCheckingSupport}"
+    "-Denable_ns3=off"
+    "-Denable_lua=off"
+    "-Denable_lib_in_jar=off"
+    "-Denable_maintainer_mode=off"
+    "-Denable_mallocators=on"
+    "-Denable_debug=on"
+    "-Denable_smpi=on"
+    "-Dminimal-bindings=${optionOnOff minimalBindings}"
+    "-Denable_smpi_ISP_testsuite=${optionOnOff moreTests}"
+    "-Denable_smpi_MPICH3_testsuite=${optionOnOff moreTests}"
+    "-Denable_compile_warnings=off"
+    "-Denable_compile_optimizations=${optionOnOff optimize}"
+    "-Denable_lto=${optionOnOff optimize}"
+  ];
+  makeFlags = optional debug "VERBOSE=1";
+
+  # needed to run tests and to ensure correct shabangs in output scripts
+  preBuild = ''
+    patchShebangs ..
+  '';
+
+  # needed by tests (so libsimgrid.so is found)
+  preConfigure = ''
+    export LD_LIBRARY_PATH="$PWD/build/lib"
+  '';
+
+  doCheck = true;
+  preCheck = ''
+    # prevent the execution of tests known to fail
+    cat <<EOW >CTestCustom.cmake
+    SET(CTEST_CUSTOM_TESTS_IGNORE smpi-replay-multiple)
+    EOW
+
+    # make sure tests are built in parallel (this can be long otherwise)
+    make tests -j $NIX_BUILD_CORES
+  '';
+
+  postInstall = lib.optionalString withoutBin ''
+    # remove bin from output if requested.
+    # having a specific bin output would be cleaner but it does not work currently (circular references)
+    rm -rf $out/bin
+  '' + lib.optionalString buildPythonBindings ''
+    # manually install the python binding if requested.
+    mkdir -p $python/lib/python${lib.versions.majorMinor python3.version}/site-packages/
+    cp ./lib/simgrid.cpython*.so $python/lib/python${lib.versions.majorMinor python3.version}/site-packages/
+   '';
+
+  # improve debuggability if requested
+  hardeningDisable = lib.optionals debug [ "fortify" ];
+  dontStrip = debug;
+
+  meta = {
+    description = "Framework for the simulation of distributed applications";
+    longDescription = ''
+      SimGrid is a toolkit that provides core functionalities for the
+      simulation of distributed applications in heterogeneous distributed
+      environments.  The specific goal of the project is to facilitate
+      research in the area of distributed and parallel application
+      scheduling on distributed computing platforms ranging from simple
+      network of workstations to Computational Grids.
+    '';
+    homepage = "https://simgrid.org/";
+    license = licenses.lgpl2Plus;
+    maintainers = with maintainers; [ mickours mpoquet ];
+    platforms = platforms.all;
+    broken = stdenv.isDarwin;
+  };
+}
--- a/pkgs/applications/science/misc/snakemake/default.nix
+++ b/pkgs/applications/science/misc/snakemake/default.nix
@ -0,0 +1,85 @@
+{ lib
+, fetchFromGitHub
+, python3
+}:
+
+python3.pkgs.buildPythonApplication rec {
+  pname = "snakemake";
+  version = "7.8.1";
+  format = "setuptools";
+
+  src = fetchFromGitHub {
+    owner = "snakemake";
+    repo = pname;
+    rev = "refs/tags/v${version}";
+    hash = "sha256-bb6bu4IiW3zaQ3PP/wgRuIwHihC5/6ZS4YSNRk3Tu4s=";
+  };
+
+  propagatedBuildInputs = with python3.pkgs; [
+    appdirs
+    configargparse
+    connection-pool
+    datrie
+    docutils
+    filelock
+    GitPython
+    jinja2
+    jsonschema
+    nbformat
+    networkx
+    psutil
+    pulp
+    pygraphviz
+    pyyaml
+    ratelimiter
+    requests
+    retry
+    smart-open
+    stopit
+    tabulate
+    toposort
+    wrapt
+    yte
+  ];
+
+  # See
+  # https://github.com/snakemake/snakemake/blob/main/.github/workflows/main.yml#L99
+  # for the current basic test suite. Tibanna and Tes require extra
+  # setup.
+
+  checkInputs = with python3.pkgs; [
+    pandas
+    pytestCheckHook
+    requests-mock
+  ];
+
+  disabledTestPaths = [
+    "tests/test_tes.py"
+    "tests/test_tibanna.py"
+    "tests/test_linting.py"
+  ];
+
+  disabledTests = [
+    # Tests require network access
+    "test_github_issue1396"
+    "test_github_issue1460"
+  ];
+
+  pythonImportsCheck = [
+    "snakemake"
+  ];
+
+  meta = with lib; {
+    homepage = "https://snakemake.github.io";
+    license = licenses.mit;
+    description = "Python-based execution environment for make-like workflows";
+    longDescription = ''
+      Snakemake is a workflow management system that aims to reduce the complexity of
+      creating workflows by providing a fast and comfortable execution environment,
+      together with a clean and readable specification language in Python style. Snakemake
+      workflows are essentially Python scripts extended by declarative code to define
+      rules. Rules describe how to create output files from input files.
+    '';
+    maintainers = with maintainers; [ helkafen renatoGarcia veprbl ];
+  };
+}
--- a/pkgs/applications/science/misc/toil/default.nix
+++ b/pkgs/applications/science/misc/toil/default.nix
@ -0,0 +1,46 @@
+{ lib
+, fetchFromGitHub
+, python3
+}:
+
+python3.pkgs.buildPythonApplication rec {
+  pname = "toil";
+  version = "5.6.0";
+  format = "setuptools";
+
+  src = python3.pkgs.fetchPypi {
+    inherit pname version;
+    sha256 = "sha256-m6tzrRCCLULO+wB8htUlt0KESLm/vdIeTzBrihnAo/I=";
+  };
+
+  propagatedBuildInputs = with python3.pkgs; [
+    addict
+    docker
+    pytz
+    pyyaml
+    enlighten
+    psutil
+    py-tes
+    python-dateutil
+    dill
+  ];
+
+  checkInputs = with python3.pkgs; [
+    pytestCheckHook
+  ];
+
+  pytestFlagsArray = [
+    "src/toil/test"
+  ];
+
+  pythonImportsCheck = [
+    "toil"
+  ];
+
+  meta = with lib; {
+    description = "Workflow engine written in pure Python";
+    homepage = "https://toil.ucsc-cgl.org/";
+    license = with licenses; [ asl20 ];
+    maintainers = with maintainers; [ veprbl ];
+  };
+}
--- a/pkgs/applications/science/misc/tulip/default.nix
+++ b/pkgs/applications/science/misc/tulip/default.nix
@ -0,0 +1,41 @@
+{ fetchurl, lib, stdenv, libxml2, freetype, libGLU, libGL, glew
+, qtbase, wrapQtAppsHook, python3
+, cmake, libjpeg }:
+
+stdenv.mkDerivation rec {
+  pname = "tulip";
+  version = "5.6.1";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/auber/${pname}-${version}_src.tar.gz";
+    sha256 = "1fy3nvgxv3igwc1d23zailcgigj1d0f2kkh7a5j24c0dyqz5zxmw";
+  };
+
+  buildInputs = [ libxml2 freetype glew libGLU libGL libjpeg qtbase python3 ];
+  nativeBuildInputs = [ cmake wrapQtAppsHook ];
+
+  qtWrapperArgs = [ ''--prefix PATH : ${lib.makeBinPath [ python3 ]}'' ];
+
+  # FIXME: "make check" needs Docbook's DTD 4.4, among other things.
+  doCheck = false;
+
+  meta = {
+    broken = (stdenv.isLinux && stdenv.isAarch64);
+    description = "A visualization framework for the analysis and visualization of relational data";
+
+    longDescription =
+      '' Tulip is an information visualization framework dedicated to the
+         analysis and visualization of relational data.  Tulip aims to
+         provide the developer with a complete library, supporting the design
+         of interactive information visualization applications for relational
+         data that can be tailored to the problems he or she is addressing.
+      '';
+
+    homepage = "http://tulip.labri.fr/";
+
+    license = lib.licenses.gpl3Plus;
+
+    maintainers = [ ];
+    platforms = lib.platforms.gnu ++ lib.platforms.linux;  # arbitrary choice
+  };
+}
--- a/pkgs/applications/science/misc/vite/default.nix
+++ b/pkgs/applications/science/misc/vite/default.nix
@ -0,0 +1,46 @@
+{ fetchsvn, lib, stdenv, cmake, qt4, libGLU, libGL }:
+
+# ViTE 1.1 has several bugs, so use the SVN version.
+let
+  rev = "1543";
+  externals = fetchsvn {
+    url = "svn://scm.gforge.inria.fr/svn/vite/externals";
+    sha256 = "1a422n3dp72v4visq5b1i21cf8sj12903sgg5v2hah3sgk02dnyz";
+    inherit rev;
+  };
+in
+stdenv.mkDerivation {
+  pname = "vite";
+  version = "1.2pre${rev}";
+
+  src = fetchsvn {
+    url = "svn://scm.gforge.inria.fr/svn/vite/trunk";
+    sha256 = "02479dv96h29d0w0svp42mjjrxhmv8lkkqp30w7mlx5gr2g0v7lf";
+    inherit rev;
+  };
+
+  preConfigure = ''
+    rm -rv externals
+    ln -sv "${externals}" externals
+  '';
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ qt4 libGLU libGL ];
+
+  NIX_LDFLAGS = "-lGLU";
+
+  meta = {
+    description = "Visual Trace Explorer (ViTE), a tool to visualize execution traces";
+
+    longDescription = ''
+      ViTE is a trace explorer. It is a tool to visualize execution
+      traces in Pajé or OTF format for debugging and profiling
+      parallel or distributed applications.
+    '';
+
+    homepage = "http://vite.gforge.inria.fr/";
+    license = lib.licenses.cecill20;
+    maintainers = with lib.maintainers; [ ];
+    platforms = lib.platforms.linux;
+  };
+}