nixpkgs/pkgs/applications/science/biology/minc-tools/default.nix

{ stdenv, fetchFromGitHub, cmake, makeWrapper, flex, bison, perl, TextFormat,
  libminc, libjpeg, nifticlib, zlib }:

stdenv.mkDerivation rec {
  pname   = "minc-tools";
  version = "unstable-2019-12-04";

  src = fetchFromGitHub {
    owner  = "BIC-MNI";
    repo   = pname;
    rev    = "d4dddfdb4e4fa0cea389b8fdce51cfc076565d94";
    sha256 = "1wwdss59qq4hz1jp35qylfswzzv0d37if23al0srnxkkgc5f8zng";
  };

  patches = [ ./fix-netcdf-header.patch ];

  nativeBuildInputs = [ cmake flex bison makeWrapper ];
  buildInputs = [ libminc libjpeg zlib ];
  propagatedBuildInputs = [ perl TextFormat ];

  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/"
                 "-DZNZ_INCLUDE_DIR=${nifticlib}/include/"
                 "-DZNZ_LIBRARY=${nifticlib}/lib/libznz.a"
                 "-DNIFTI_INCLUDE_DIR=${nifticlib}/include/nifti/"
                 "-DNIFTI_LIBRARY=${nifticlib}/lib/libniftiio.a" ];

  postFixup = ''
    for prog in minccomplete minchistory mincpik; do
      wrapProgram $out/bin/$prog --prefix PERL5LIB : $PERL5LIB
    done
  '';

  enableParallelBuilding = true;

  meta = with stdenv.lib; {
    homepage = https://github.com/BIC-MNI/minc-tools;
    description = "Command-line utilities for working with MINC files";
    maintainers = with maintainers; [ bcdarwin ];
    platforms = platforms.unix;
    license   = licenses.free;
  };
}