# 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; {

  blast = callPackage ./blast {
    stdenv = overrideCC stdenv gcc5;
    boost = boost162;
  };

  cloudcompare = libsForQt5.callPackage ./cloudcompare.nix { boost = boost15x; };

  cryptominisat = callPackage ./cryptominisat.nix { python = python27; };

  #firedrake = callPackage ./firedrake { };

  inherit (callPackages ./octopus/libxc.nix { }) libxc301 libxc404;
  libxc3 = libxc301;
  libxc4 = libxc404;
  libxc = libxc4;

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

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

  inherit (callPackages ./octopus/octopus.nix { stdenv = overrideCC stdenv gcc5; gfortran = gfortran5; }) octopus72;
  octopus7 = octopus72;
  octopus = octopus7;

  openfoam = callPackage ./openfoam.nix { };

  openslide = callPackage ./openslide { };
  openslide-python = callPackage ./openslide/python.nix { pythonPackages = python27Packages; };

  ovito = libsForQt5.callPackage ./ovito.nix { stdenv = overrideCC stdenv gcc6; };

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

  namd = callPackage ./namd.nix { };

  sambamba = callPackage ./sambamba.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 ]; } );
}