depot/third_party/nixpkgs/pkgs/applications/science/biology/samtools/default.nix

{ stdenv, fetchurl, zlib, htslib, perl, ncurses ? null }:

stdenv.mkDerivation rec {
  pname = "samtools";
  version = "1.11";

  src = fetchurl {
    url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2";
    sha256 = "1dp5wknak4arnw5ghhif9mmljlfnw5bgm91wib7z0j8wdjywx0z2";
  };

  nativeBuildInputs = [ perl ];

  buildInputs = [ zlib ncurses htslib ];

  configureFlags = [ "--with-htslib=${htslib}" ]
    ++ stdenv.lib.optional (ncurses == null) "--without-curses";

  preCheck = ''
    patchShebangs test/
  '';

  enableParallelBuilding = true;

  doCheck = true;

  meta = with stdenv.lib; {
    description = "Tools for manipulating SAM/BAM/CRAM format";
    license = licenses.mit;
    homepage = "http://www.htslib.org/";
    platforms = platforms.unix;
    maintainers = with maintainers; [ mimame unode ];
  };
}