rtg-tools: init at 3.12.1

{

  lib,

  stdenv,

  fetchFromGitHub,

  jdk,

  ant,

  git,

  unzip,

}:

stdenv.mkDerivation rec {

  pname = "rtg-tools";

  version = "3.12.1";

  src = fetchFromGitHub {

    owner = "RealTimeGenomics";

    repo = "rtg-tools";

    rev = version;

    sha256 = "sha256-fMrrjrgaGxBVxn6qMq2g0oFv6qtfhZcQlkvv1E9Os6Y=";

  };

  nativeBuildInputs = [

    ant

    jdk

    git # Required by build.xml to manage the build revision

    unzip

  ];

  buildPhase = ''

    runHook preBuild

    ant rtg-tools.jar

    runHook postBuild

  '';

  installPhase = ''

    runHook preInstall

    mkdir -p $out/bin

    cp build/rtg-tools.jar $out/bin/RTG.jar

    cp installer/rtg $out/bin/

    runHook postInstall

  '';

  postPatch = ''

    # Use a location outside nix (must be writable)

    substituteInPlace installer/rtg \

      --replace-fail  '$THIS_DIR/rtg.cfg' '$HOME/.config/rtg-tools/rtg.cfg'  \

      --replace-fail 'RTG_JAVA="java"' 'RTG_JAVA="${jdk}/lib/openjdk/bin/java"'

    sed -i '/USER_JAVA_OPTS=$RTG_JAVA_OPTS/a mkdir -p $HOME/.config/rtg-tools'  installer/rtg

  '';

  meta = with lib; {

    homepage = "https://github.com/RealTimeGenomics/rtg-tools";

    description = "Useful utilities for dealing with VCF files and sequence data, especially vcfeval";

    license = licenses.bsd2;

    platforms = [ "x86_64-linux" ];

    maintainers = with maintainers; [ apraga ];

  };

}