trimmomatic: 0.39 -> 0.40 (#435542)

{

  lib,

  stdenv,

  fetchFromGitHub,

  ant,

  jdk21_headless,

  jre_minimal,

  makeWrapper,

  stripJavaArchivesHook,

  maven,

  nix-update-script,

}:

let

  jdk = jdk21_headless;

  # Reduce closure size

  jre = jre_minimal.override {

    modules = [

      "java.base"

      "java.logging"

    ];

    jdk = jdk21_headless;

  };

in

stdenv.mkDerivation (finalAttrs: {

maven.buildMavenPackage rec {

  pname = "trimmomatic";

  version = "0.39";

  version = "0.40";

  src = fetchFromGitHub {

    owner = "usadellab";

    repo = "Trimmomatic";

    rev = "v${finalAttrs.version}";

    hash = "sha256-u+ubmacwPy/vsEi0YQCv0fTnVDesQvqeQDEwCbS8M6I=";

    rev = "v${version}";

    hash = "sha256-pLUjSVePN++G2XZrdKEdobgBO+UD0PZ9wlhSUlZ7na8=";

  };

  # Remove jdk version requirement

  postPatch = ''

    substituteInPlace ./build.xml \

      --replace 'source="1.5" target="1.5"' ""

  '';

  mvnHash = "sha256-1XnVdud8nI2SuEPXnwEmbudM+QAeoSVTn0UZ8PKJH44=";

  nativeBuildInputs = [

    ant

    jdk

    makeWrapper

    stripJavaArchivesHook

  ];

  buildPhase = ''

    runHook preBuild

    ant

    runHook postBuild

  '';

  installPhase = ''

    runHook preInstall

    install -Dm644 dist/jar/trimmomatic-*.jar -t $out/share/trimmomatic

    install -Dm644 target/trimmomatic-${version}.jar -t $out/share/trimmomatic

    cp -r adapters $out/share/trimmomatic

    makeWrapper ${jre}/bin/java $out/bin/trimmomatic \

        --add-flags "-jar $out/share/trimmomatic/trimmomatic-*.jar"

    makeWrapper ${lib.getBin jre_minimal}/bin/java $out/bin/trimmomatic \

        --add-flags "-jar $out/share/trimmomatic/trimmomatic-${version}.jar"

    runHook postInstall

  '';

  passthru = {

    updateScript = nix-update-script { };

  };

  meta = {

    changelog = "https://github.com/usadellab/Trimmomatic/blob/main/versionHistory.txt";

    changelog = "https://github.com/usadellab/Trimmomatic/releases/tag/v${version}";

    description = "Flexible read trimming tool for Illumina NGS data";

    longDescription = ''

      Trimmomatic performs a variety of useful trimming tasks for illumina

    mainProgram = "trimmomatic";

    maintainers = [ lib.maintainers.kupac ];

  };

})

}