Merge staging-next into staging

40 files changed, 801 insertions, 381 deletions

diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix
index 7e2fe48a6f4f..8d047db0e00c 100644
--- a/maintainers/maintainer-list.nix
+++ b/maintainers/maintainer-list.nix
@@ -1822,6 +1822,12 @@
     githubId = 18535642;
     name = "Emily";
   };
+  endocrimes = {
+    email = "dani@builds.terrible.systems";
+    github = "endocrimes";
+    githubId = 1330683;
+    name = "Danielle Lancashire";
+  };
   ederoyd46 = {
     email = "matt@ederoyd.co.uk";
     github = "ederoyd46";
diff --git a/nixos/modules/module-list.nix b/nixos/modules/module-list.nix
index 22fd5d7609df..b6c946b99e00 100644
--- a/nixos/modules/module-list.nix
+++ b/nixos/modules/module-list.nix
@@ -152,12 +152,14 @@
   ./programs/tmux.nix
   ./programs/tsm-client.nix
   ./programs/udevil.nix
+  ./programs/usbtop.nix
   ./programs/venus.nix
   ./programs/vim.nix
   ./programs/wavemon.nix
   ./programs/way-cooler.nix
   ./programs/waybar.nix
   ./programs/wireshark.nix
+  ./programs/x2goserver.nix
   ./programs/xfs_quota.nix
   ./programs/xonsh.nix
   ./programs/xss-lock.nix
diff --git a/nixos/modules/programs/usbtop.nix b/nixos/modules/programs/usbtop.nix
new file mode 100644
index 000000000000..c1b6ee38caa1
--- /dev/null
+++ b/nixos/modules/programs/usbtop.nix
@@ -0,0 +1,21 @@
+{ config, pkgs, lib, ... }:
+
+with lib;
+
+let
+  cfg = config.programs.usbtop;
+in {
+  options = {
+    programs.usbtop.enable = mkEnableOption "usbtop and required kernel module";
+  };
+
+  config = mkIf cfg.enable {
+    environment.systemPackages = with pkgs; [
+      usbtop
+    ];
+
+    boot.kernelModules = [
+      "usbmon"
+    ];
+  };
+}
diff --git a/nixos/modules/programs/x2goserver.nix b/nixos/modules/programs/x2goserver.nix
new file mode 100644
index 000000000000..d9e7b6e4a5c0
--- /dev/null
+++ b/nixos/modules/programs/x2goserver.nix
@@ -0,0 +1,148 @@
+{ config, lib, pkgs, ... }:
+
+with lib;
+
+let
+  cfg = config.programs.x2goserver;
+
+  defaults = {
+    superenicer = { "enable" = cfg.superenicer.enable; };
+  };
+  confText = generators.toINI {} (recursiveUpdate defaults cfg.settings);
+  x2goServerConf = pkgs.writeText "x2goserver.conf" confText;
+
+  x2goAgentOptions = pkgs.writeText "x2goagent.options" ''
+    X2GO_NXOPTIONS=""
+    X2GO_NXAGENT_DEFAULT_OPTIONS="${concatStringsSep " " cfg.nxagentDefaultOptions}"
+  '';
+
+in {
+  options.programs.x2goserver = {
+    enable = mkEnableOption "x2goserver" // {
+      description = ''
+        Enables the x2goserver module.
+        NOTE: This will create a good amount of symlinks in `/usr/local/bin`
+      '';
+    };
+
+    superenicer = {
+      enable = mkEnableOption "superenicer" // {
+        description = ''
+          Enables the SupeReNicer code in x2gocleansessions, this will renice
+          suspended sessions to nice level 19 and renice them to level 0 if the
+          session becomes marked as running again
+        '';
+      };
+    };
+
+    nxagentDefaultOptions = mkOption {
+      type = types.listOf types.str;
+      default = [ "-extension GLX" "-nolisten tcp" ];
+      example = [ "-extension GLX" "-nolisten tcp" ];
+      description = ''
+        List of default nx agent options.
+      '';
+    };
+
+    settings = mkOption {
+      type = types.attrsOf types.attrs;
+      default = {};
+      description = ''
+        x2goserver.conf ini configuration as nix attributes. See
+        `x2goserver.conf(5)` for details
+      '';
+      example = literalExample ''
+        superenicer = {
+          "enable" = "yes";
+          "idle-nice-level" = 19;
+        };
+        telekinesis = { "enable" = "no"; };
+      '';
+    };
+  };
+
+  config = mkIf cfg.enable {
+
+    environment.systemPackages = [ pkgs.x2goserver ];
+
+    users.groups.x2go = {};
+    users.users.x2go = {
+      home = "/var/lib/x2go/db";
+      group = "x2go";
+    };
+
+    security.wrappers.x2gosqliteWrapper = {
+      source = "${pkgs.x2goserver}/lib/x2go/libx2go-server-db-sqlite3-wrapper.pl";
+      owner = "x2go";
+      group = "x2go";
+      setgid = true;
+    };
+    security.wrappers.x2goprintWrapper = {
+      source = "${pkgs.x2goserver}/bin/x2goprint";
+      owner = "x2go";
+      group = "x2go";
+      setgid = true;
+    };
+
+    systemd.tmpfiles.rules = with pkgs; [
+      "d /var/lib/x2go/ - x2go x2go - -"
+      "d /var/lib/x2go/db - x2go x2go - -"
+      "d /var/lib/x2go/conf - x2go x2go - -"
+      "d /run/x2go 0755 x2go x2go - -"
+    ] ++
+    # x2goclient sends SSH commands with preset PATH set to
+    # "/usr/local/bin;/usr/bin;/bin". Since we cannot filter arbitrary ssh
+    # commands, we have to make the following executables available.
+    map (f: "L+ /usr/local/bin/${f} - - - - ${x2goserver}/bin/${f}") [
+      "x2goagent" "x2gobasepath" "x2gocleansessions" "x2gocmdexitmessage"
+      "x2godbadmin" "x2gofeature" "x2gofeaturelist" "x2gofm" "x2gogetapps"
+      "x2gogetservers" "x2golistdesktops" "x2golistmounts" "x2golistsessions"
+      "x2golistsessions_root" "x2golistshadowsessions" "x2gomountdirs"
+      "x2gopath" "x2goprint" "x2goresume-desktopsharing" "x2goresume-session"
+      "x2goruncommand" "x2goserver-run-extensions" "x2gosessionlimit"
+      "x2gosetkeyboard" "x2goshowblocks" "x2gostartagent"
+      "x2gosuspend-desktopsharing" "x2gosuspend-session"
+      "x2goterminate-desktopsharing" "x2goterminate-session"
+      "x2goumount-session" "x2goversion"
+    ] ++ [
+      "L+ /usr/local/bin/awk - - - - ${gawk}/bin/awk"
+      "L+ /usr/local/bin/chmod - - - - ${coreutils}/bin/chmod"
+      "L+ /usr/local/bin/cp - - - - ${coreutils}/bin/cp"
+      "L+ /usr/local/bin/sed - - - - ${gnused}/bin/sed"
+      "L+ /usr/local/bin/setsid - - - - ${utillinux}/bin/setsid"
+      "L+ /usr/local/bin/xrandr - - - - ${xorg.xrandr}/bin/xrandr"
+      "L+ /usr/local/bin/xmodmap - - - - ${xorg.xmodmap}/bin/xmodmap"
+    ];
+
+    systemd.services.x2goserver = {
+      description = "X2Go Server Daemon";
+      wantedBy = [ "multi-user.target" ];
+      unitConfig.Documentation = "man:x2goserver.conf(5)";
+      serviceConfig = {
+        Type = "forking";
+        ExecStart = "${pkgs.x2goserver}/bin/x2gocleansessions";
+        PIDFile = "/run/x2go/x2goserver.pid";
+        User = "x2go";
+        Group = "x2go";
+        RuntimeDirectory = "x2go";
+        StateDirectory = "x2go";
+      };
+      preStart = ''
+        if [ ! -e /var/lib/x2go/setup_ran ]
+        then
+          mkdir -p /var/lib/x2go/conf
+          cp -r ${pkgs.x2goserver}/etc/x2go/* /var/lib/x2go/conf/
+          ln -sf ${x2goServerConf} /var/lib/x2go/conf/x2goserver.conf
+          ln -sf ${x2goAgentOptions} /var/lib/x2go/conf/x2goagent.options
+          ${pkgs.x2goserver}/bin/x2godbadmin --createdb
+          touch /var/lib/x2go/setup_ran
+        fi
+      '';
+    };
+
+    # https://bugs.x2go.org/cgi-bin/bugreport.cgi?bug=276
+    security.sudo.extraConfig = ''
+      Defaults  env_keep+=QT_GRAPHICSSYSTEM
+    '';
+  };
+}
diff --git a/nixos/modules/services/networking/bitcoind.nix b/nixos/modules/services/networking/bitcoind.nix
index d3501636b41d..1439d739da9d 100644
--- a/nixos/modules/services/networking/bitcoind.nix
+++ b/nixos/modules/services/networking/bitcoind.nix
@@ -59,8 +59,8 @@ in {
 
       package = mkOption {
         type = types.package;
-        default = pkgs.altcoins.bitcoind;
-        defaultText = "pkgs.altcoins.bitcoind";
+        default = pkgs.bitcoind;
+        defaultText = "pkgs.bitcoind";
         description = "The package providing bitcoin binaries.";
       };
       configFile = mkOption {
diff --git a/nixos/modules/services/networking/namecoind.nix b/nixos/modules/services/networking/namecoind.nix
index a569ca87e262..c8ee0a2f5647 100644
--- a/nixos/modules/services/networking/namecoind.nix
+++ b/nixos/modules/services/networking/namecoind.nix
@@ -175,7 +175,7 @@ in
       serviceConfig = {
         User  = "namecoin";
         Group = "namecoin";
-        ExecStart  = "${pkgs.altcoins.namecoind}/bin/namecoind -conf=${configFile} -datadir=${dataDir} -printtoconsole";
+        ExecStart  = "${pkgs.namecoind}/bin/namecoind -conf=${configFile} -datadir=${dataDir} -printtoconsole";
         ExecStop   = "${pkgs.coreutils}/bin/kill -KILL $MAINPID";
         ExecReload = "${pkgs.coreutils}/bin/kill -HUP $MAINPID";
         Nice = "10";
diff --git a/pkgs/applications/misc/yubioath-desktop/default.nix b/pkgs/applications/misc/yubioath-desktop/default.nix
index 843bc0c1c234..d7a019c1c416 100644
--- a/pkgs/applications/misc/yubioath-desktop/default.nix
+++ b/pkgs/applications/misc/yubioath-desktop/default.nix
@@ -44,6 +44,7 @@ mkDerivation rec {
       cp resources/icons/*.{icns,ico,png,xpm} $out/share/yubioath/icons
       substituteInPlace $out/share/applications/yubioath-desktop.desktop \
         --replace 'Exec=yubioath-desktop' "Exec=$out/bin/yubioath-desktop" \
+        --replace 'Icon=yubioath' "Icon=$out/share/yubioath/icons/yubioath.png"
   '';
 
   meta = with stdenv.lib; {
diff --git a/pkgs/applications/networking/flent/default.nix b/pkgs/applications/networking/flent/default.nix
index bc0a519a0eee..bbd9a7601acd 100644
--- a/pkgs/applications/networking/flent/default.nix
+++ b/pkgs/applications/networking/flent/default.nix
@@ -1,30 +1,39 @@
-{ stdenv, buildPythonApplication, fetchFromGitHub, matplotlib, procps, pyqt5
-, sphinx
-}:
+{ stdenv, buildPythonApplication, fetchPypi, matplotlib, procps, pyqt5, python
+, pythonPackages, qt5, sphinx, xvfb_run }:
 
 buildPythonApplication rec {
   pname = "flent";
-  version = "1.2.2";
-  src = fetchFromGitHub {
-    owner = "tohojo";
-    repo = "flent";
-    rev = "v${version}";
-    sha256 = "1llcdakk0nk9xlpjjz7mv4a80yq4sjnbqhaqvyj9m6lbcxgssh2r";
+  version = "1.3.0";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "099779i0ghjd9ikq77z6m6scnlmk946lw9issrgz8zm7babiw4d7";
   };
 
   buildInputs = [ sphinx ];
+  nativeBuildInputs = [ qt5.wrapQtAppsHook ];
+  propagatedBuildInputs = [ matplotlib procps pyqt5 ];
+  checkInputs = [ procps pythonPackages.mock pyqt5 xvfb_run ];
 
-  checkInputs = [ procps ];
+  checkPhase = ''
+    cat >test-runner <<EOF
+    #!/bin/sh
 
-  propagatedBuildInputs = [
-    matplotlib
-    procps
-    pyqt5
-  ];
+    ${python.pythonForBuild.interpreter} nix_run_setup test
+    EOF
+    chmod +x test-runner
+    wrapQtApp test-runner --prefix PYTHONPATH : $PYTHONPATH
+    xvfb-run -s '-screen 0 800x600x24' ./test-runner
+  '';
+
+  postInstall = ''
+    for program in $out/bin/*; do
+      wrapQtApp $program --prefix PYTHONPATH : $PYTHONPATH
+    done
+  '';
 
   meta = with stdenv.lib; {
     description = "The FLExible Network Tester";
-    homepage = https://flent.org;
+    homepage = "https://flent.org";
     license = licenses.gpl3;
 
     maintainers = [ maintainers.mmlb ];
diff --git a/pkgs/applications/networking/instant-messengers/discord/default.nix b/pkgs/applications/networking/instant-messengers/discord/default.nix
index 189092a6d5e0..1d9d645b0ed5 100644
--- a/pkgs/applications/networking/instant-messengers/discord/default.nix
+++ b/pkgs/applications/networking/instant-messengers/discord/default.nix
@@ -27,10 +27,10 @@ in {
     pname = "discord-canary";
     binaryName = "DiscordCanary";
     desktopName = "Discord Canary";
-    version = "0.0.93";
+    version = "0.0.95";
     src = fetchurl {
-      url = "https://dl-canary.discordapp.net/apps/linux/0.0.93/discord-canary-0.0.93.tar.gz";
-      sha256 = "1jzm5fm7a1p68ims7bv5am0bpbvrhbynzblpj9qrzzrwakdaywbi";
+      url = "https://dl-canary.discordapp.net/apps/linux/0.0.95/discord-canary-0.0.95.tar.gz";
+      sha256 = "06qhm73kc88pq0lgbi7qjy4gx9ighkmx128fdm1dpzfv62fjdasw";
     };
   };
 }.${branch}
diff --git a/pkgs/applications/networking/instant-messengers/mattermost-desktop/default.nix b/pkgs/applications/networking/instant-messengers/mattermost-desktop/default.nix
index 6f4e7e5b677b..f5f8414c870c 100644
--- a/pkgs/applications/networking/instant-messengers/mattermost-desktop/default.nix
+++ b/pkgs/applications/networking/instant-messengers/mattermost-desktop/default.nix
@@ -38,18 +38,18 @@ let
 in
   stdenv.mkDerivation rec {
     pname = "mattermost-desktop";
-    version = "4.2.0";
+    version = "4.2.3";
 
     src =
       if stdenv.hostPlatform.system == "x86_64-linux" then
         fetchurl {
           url = "https://releases.mattermost.com/desktop/${version}/${pname}-${version}-linux-x64.tar.gz";
-          sha256 = "0hka94gwpscjn61032c0grpjv5gjb0j8rkx6pgwci617n29xkyf6";
+          sha256 = "14xyn8dp0xxl4j9xdsjik9p6srqdxbirgcgym2sv64p01w3kc9wf";
         }
       else if stdenv.hostPlatform.system == "i686-linux" then
         fetchurl {
           url = "https://releases.mattermost.com/desktop/${version}/${pname}-${version}-linux-ia32.tar.gz";
-          sha256 = "1nx2sgbnr60h6kn56wv54m7cvyx27d64bfprpb94hqd5c2z21x80";
+          sha256 = "063rrxw76mjz71wp9xd3ppkq3s017vrzms879r2cilypmay7fhgs";
         }
       else
         throw "Mattermost-Desktop is not currently supported on ${stdenv.hostPlatform.system}";
diff --git a/pkgs/applications/networking/remote/x2goserver/default.nix b/pkgs/applications/networking/remote/x2goserver/default.nix
new file mode 100644
index 000000000000..f69d2326217d
--- /dev/null
+++ b/pkgs/applications/networking/remote/x2goserver/default.nix
@@ -0,0 +1,93 @@
+{ stdenv, lib, fetchurl, perlPackages, makeWrapper, perl, which, nx-libs
+, utillinux, coreutils, glibc, gawk, gnused, gnugrep, findutils, xorg
+, nettools, iproute, bc, procps, psmisc, lsof, pwgen, openssh, sshfs, bash
+}:
+
+let
+  pname = "x2goserver";
+  version = "4.1.0.3";
+
+  src = fetchurl {
+    url = "http://code.x2go.org/releases/source/x2goserver/${pname}-${version}.tar.gz";
+    sha256 = "1l6wd708kbipib4ldprfiihqmj4895nifg0bkws4x97majislxk7";
+  };
+
+  x2go-perl = perlPackages.buildPerlPackage rec {
+    pname = "X2Go";
+    inherit version src;
+    makeFlags = [ "-f" "Makefile.perl" ];
+    patchPhase = ''
+      substituteInPlace X2Go/Config.pm --replace '/etc/x2go' '/var/lib/x2go/conf'
+      substituteInPlace X2Go/Server/DB.pm \
+        --replace '$x2go_lib_path/libx2go-server-db-sqlite3-wrapper' \
+                  '/run/wrappers/bin/x2gosqliteWrapper'
+      substituteInPlace X2Go/Server/DB/SQLite3.pm --replace "user='x2gouser'" "user='x2go'"
+    '';
+  };
+
+  perlEnv = perl.withPackages (p: with p; [
+    x2go-perl DBI DBDSQLite FileBaseDir TryTiny CaptureTiny ConfigSimple Switch
+  ]);
+
+  binaryDeps = [
+    perlEnv which nx-libs utillinux coreutils glibc.bin gawk gnused gnugrep
+    findutils nettools iproute bc procps psmisc lsof pwgen openssh sshfs
+    xorg.xauth xorg.xinit xorg.xrandr xorg.xmodmap xorg.xwininfo xorg.fontutil
+    xorg.xkbcomp xorg.setxkbmap
+  ];
+in
+stdenv.mkDerivation rec {
+  inherit pname version src;
+
+  buildInputs = [ perlEnv bash ];
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  prePatch = ''
+    patchShebangs .
+    sed -i '/Makefile.PL\|Makefile.perl/d' Makefile
+    for i in */Makefile; do
+      substituteInPlace "$i" --replace "-o root -g root " ""
+    done
+    substituteInPlace libx2go-server-db-perl/Makefile --replace "chmod 2755" "chmod 755"
+    for i in x2goserver/sbin/x2godbadmin x2goserver/bin/x2go*
+    do
+      substituteInPlace $i --replace '/etc/x2go' '/var/lib/x2go/conf'
+    done
+    substituteInPlace x2goserver/sbin/x2gocleansessions \
+      --replace '/var/run/x2goserver.pid' '/var/run/x2go/x2goserver.pid'
+    substituteInPlace x2goserver/sbin/x2godbadmin --replace 'user="x2gouser"' 'user="x2go"'
+    substituteInPlace x2goserver-xsession/etc/Xsession \
+      --replace "SSH_AGENT /bin/bash -c" "SSH_AGENT ${bash}/bin/bash -c" \
+      --replace "[ -f /etc/redhat-release ]" "[ -d /etc/nix ] || [ -f /etc/redhat-release ]"
+  '';
+
+  makeFlags = [ "PREFIX=/" "NXLIBDIR=${nx-libs}/lib/nx" ];
+
+  installFlags = [ "DESTDIR=$(out)" ];
+
+  postInstall = ''
+    mv $out/etc/x2go/x2goserver.conf{,.example}
+    mv $out/etc/x2go/x2goagent.options{,.example}
+    ln -sf ${nx-libs}/bin/nxagent $out/bin/x2goagent
+    for i in $out/sbin/x2go* $(find $out/bin -type f) \
+      $(ls $out/lib/x2go/x2go* | grep -v x2gocheckport)
+    do
+      wrapProgram $i --prefix PATH : ${lib.makeBinPath binaryDeps}:$out
+    done
+    # We're patching @INC of the setgid wrapper, because we can't mix
+    # the perl wrapper (for PERL5LIB) with security.wrappers (for setgid)
+    sed -ie "s,.\+bin/perl,#!${perl}/bin/perl -I ${perlEnv}/lib/perl5/site_perl," \
+      $out/lib/x2go/libx2go-server-db-sqlite3-wrapper.pl
+  '';
+
+  enableParallelBuilding = true;
+
+  meta = with stdenv.lib; {
+    description = "Remote desktop application, server component";
+    homepage = "http://x2go.org/";
+    platforms = stdenv.lib.platforms.linux;
+    license = licenses.gpl2;
+    maintainers = [ maintainers.averelld ];
+  };
+}
diff --git a/pkgs/applications/science/biology/trimal/default.nix b/pkgs/applications/science/biology/trimal/default.nix
new file mode 100755
index 000000000000..d4e8fee7bc36
--- /dev/null
+++ b/pkgs/applications/science/biology/trimal/default.nix
@@ -0,0 +1,31 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  pname = "trimal";
+  version = "1.4.1";
+
+  src = fetchFromGitHub {
+    repo = pname;
+    owner = "scapella";
+    rev = "v${version}";
+    sha256 = "0isc7s3514di4z953xq53ncjkbi650sh4q9yyw5aag1n9hqnh7k0";
+  };
+
+  postUnpack = ''
+    sourceRoot=''${sourceRoot}/source
+    echo Source root reset to ''${sourceRoot}
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp -a trimal readal statal $out/bin
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment";
+    license = licenses.gpl3;
+    platforms = platforms.linux;
+    homepage = http://trimal.cgenomics.org;
+    maintainers = [ maintainers.bzizou ];
+  };
+}
diff --git a/pkgs/applications/science/math/pari/default.nix b/pkgs/applications/science/math/pari/default.nix
index 72827112c50c..89ae354e7c76 100644
--- a/pkgs/applications/science/math/pari/default.nix
+++ b/pkgs/applications/science/math/pari/default.nix
@@ -1,6 +1,5 @@
 { stdenv
 , fetchurl
-, fetchpatch
 , gmp
 , readline
 , libX11
@@ -13,25 +12,13 @@ assert withThread -> libpthreadstubs != null;
 
 stdenv.mkDerivation rec {
   pname = "pari";
-  version = "2.11.1";
+  version = "2.11.2";
 
   src = fetchurl {
     url = "https://pari.math.u-bordeaux.fr/pub/pari/unix/${pname}-${version}.tar.gz";
-    sha256 = "1jfax92jpydjd02fwl30r6b8kfzqqd6sm4yx94gidyz9lqjb7a94";
+    sha256 = "0fck8ssmirl8fy7s4mspgrxjs5sag76xbshqlqzkcl3kqyrk4raa";
   };
 
-  patches = [
-    # Fix a off-by-one bug that can potentially lead to segfaults (accepted upstream)
-    # https://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=2117
-    # https://trac.sagemath.org/ticket/27335
-    (fetchpatch {
-      name = "fix-off-by-one-error.patch";
-      # only relevant parts of https://pari.math.u-bordeaux.fr/cgi-bin/gitweb.cgi?p=pari.git;a=patch;h=aa1ee6e0898d177e6bcf49237d82c804bc410985
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pari/patches/red_montgomery.patch?id=bbea55c96e1f05302b3c7f593cf64492497047c5";
-      sha256 = "0vqkmhgv9splsdswp6zjnkj50z76rc1m6k9iy3cf9dxwqw3h3nr6";
-    })
-  ];
-
   buildInputs = [
     gmp
     readline
diff --git a/pkgs/applications/science/misc/colmap/default.nix b/pkgs/applications/science/misc/colmap/default.nix
new file mode 100644
index 000000000000..672569ed1002
--- /dev/null
+++ b/pkgs/applications/science/misc/colmap/default.nix
@@ -0,0 +1,37 @@
+{ mkDerivation, lib, fetchFromGitHub, cmake, boost, ceres-solver, eigen,
+  freeimage, glog, libGLU, glew, qtbase,
+  cudaSupport ? false, cudatoolkit ? null }:
+
+assert !cudaSupport || cudatoolkit != null;
+
+let boost_static = boost.override { enableStatic = true; };
+in 
+mkDerivation rec {
+  version = "3.5";
+  pname = "colmap";
+  src = fetchFromGitHub {
+     owner = "colmap";
+     repo = "colmap";
+     rev = version;
+     sha256 = "1vnb62p0y2bnga173wmjs0lnyqdjikv0fkcxjzxm8187khk2lly8";
+  };
+  
+  buildInputs = [
+    boost_static ceres-solver eigen
+    freeimage glog libGLU glew qtbase
+  ] ++ lib.optional cudaSupport cudatoolkit;
+
+  nativeBuildInputs = [ cmake ];
+
+  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.bsd2;
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ lebastr ];
+  };
+}
diff --git a/pkgs/development/compilers/glslang/default.nix b/pkgs/development/compilers/glslang/default.nix
index 79ad90e77a6e..161e57b54792 100644
--- a/pkgs/development/compilers/glslang/default.nix
+++ b/pkgs/development/compilers/glslang/default.nix
@@ -1,16 +1,29 @@
-{ stdenv, fetchFromGitHub, cmake, bison, jq, python, spirv-tools, spirv-headers }:
+{ stdenv, fetchFromGitHub
+, bison
+, cmake
+, jq
+, python3
+, spirv-headers
+, spirv-tools
+}:
+
 stdenv.mkDerivation rec {
   pname = "glslang";
-  version = "7.11.3113";
+  version = "7.11.3214";
 
   src = fetchFromGitHub {
     owner = "KhronosGroup";
     repo = "glslang";
-    rev = "${version}";
-    sha256 = "1kzv2b4q1fddxd7c0hc754nd6rw6y9vijb9fsi13xzzq9dficgb6";
+    rev = version;
+    sha256 = "0dqjga0lcza006fhac26zp2plbq4gx8a6nsmrwkqlzji6lw1jins";
+  };
+
+  # These get set at all-packages, keep onto them for child drvs
+  passthru = {
+    inherit spirv-tools spirv-headers;
   };
 
-  nativeBuildInputs = [ cmake python bison jq ];
+  nativeBuildInputs = [ cmake python3 bison jq ];
   enableParallelBuilding = true;
 
   postPatch = ''
@@ -18,6 +31,7 @@ stdenv.mkDerivation rec {
     ln -s "${spirv-headers.src}" External/spirv-tools/external/spirv-headers
   '';
 
+  # Ensure spirv-headers and spirv-tools match exactly to what is expected
   preConfigure = ''
     HEADERS_COMMIT=$(jq -r < known_good.json '.commits|map(select(.name=="spirv-tools/external/spirv-headers"))[0].commit')
     TOOLS_COMMIT=$(jq -r < known_good.json '.commits|map(select(.name=="spirv-tools"))[0].commit')
diff --git a/pkgs/development/libraries/opencv/3.x.nix b/pkgs/development/libraries/opencv/3.x.nix
index d7f897ebcf83..d8946dae095b 100644
--- a/pkgs/development/libraries/opencv/3.x.nix
+++ b/pkgs/development/libraries/opencv/3.x.nix
@@ -14,7 +14,8 @@
 , enableOpenblas  ? true, openblas
 , enableContrib   ? true
 
-, enableCuda      ? config.cudaSupport or false, cudatoolkit
+, enableCuda      ? (config.cudaSupport or false) &a