# self  - next package set (after our additions)
# super - prior package set (before our additions)
# pkgs  - final package set (after everyone's additions)
#
self: super: pkgs: with pkgs; {

  fastqc = callPackage ./fastqc.nix { };

  #firedrake = callPackage ./firedrake { };

  ghmm = callPackage ./ghmm { };

  gsort = callPackage ./gsort { };

  lumpy = callPackage ./lumpy.nix { };

  #meraculous = callPackage ./meraculous.nix { let stdenv49 = overrideCC stdenv gcc49; in stdenv = stdenv49; boost = boost159.override { stdenv = stdenv49 }; };

  mfixgui = python36Packages.callPackage ./mfix/mfixgui.nix { };
  mfixsolver = callPackage ./mfix/mfixsolver.nix { };

  inherit (callPackage ./opengl/default.nix { inherit super; }) libGL mesa_glxgallium;

  openfoam = callPackage ./openfoam.nix { };

  openslide = callPackage ./openslide { };

  ovito = libsForQt5.callPackage ./ovito.nix { };

  pythonOverrides = lib.composeExtensions super.pythonOverrides (import ./python-packages.nix pkgs);

  rOverrides = lib.composeExtensions super.rOverrides (import ./r-modules.nix pkgs);

  smoove = callPackage ./smoove { };

  #sumo = callPackage ./sumo.nix { fox = fox_1_6; };

  namd = callPackage ./namd.nix { };

  sambamba = callPackage ./sambamba.nix { };

  samblaster = callPackage ./samblaster.nix { };

  svtyper = pythonPackages.callPackage ./svtyper.nix { };

  idba = callPackage ./idba.nix { };

  nixStable = ( super.nixStable.override { confDir= "/nix/etc"; } ).overrideAttrs
    ( attrs: { patches = attrs.patches or [] ++ [ ./nix/remote.patch ./nix/cvmfs.patch ]; } );
  nix = ( super.nix.override { confDir = "/nix/etc"; } ).overrideAttrs
    ( attrs: { patches = attrs.patches or [] ++ [ ./nix/remote.patch ./nix/cvmfs.patch ]; } );
}