nextflow: 22.10.6 -> 24.08.0-edge + remove buildFHSEnv + compile from source + add tests (#339197)

  # TODO: put in networking.nix after the test becomes more complete

  networkingProxy = handleTest ./networking-proxy.nix {};

  nextcloud = handleTest ./nextcloud {};

  nextflow = handleTestOn ["x86_64-linux"] ./nextflow.nix {};

  nextjs-ollama-llm-ui = runTest ./web-apps/nextjs-ollama-llm-ui.nix;

  nexus = handleTest ./nexus.nix {};

  # TODO: Test nfsv3 + Kerberos

import ./make-test-python.nix (

  { pkgs, ... }:

  let

    bash = pkgs.dockerTools.pullImage {

      imageName = "quay.io/nextflow/bash";

      imageDigest = "sha256:bea0e244b7c5367b2b0de687e7d28f692013aa18970941c7dd184450125163ac";

      sha256 = "161s9f24njjx87qrwq0c9nmnwvyc6iblcxka7hirw78lm7i9x4w5";

      finalImageName = "quay.io/nextflow/bash";

    };

    hello = pkgs.stdenv.mkDerivation {

      name = "nextflow-hello";

      src = pkgs.fetchFromGitHub {

        owner = "nextflow-io";

        repo = "hello";

        rev = "afff16a9b45c8e8a4f5a3743780ac13a541762f8";

        hash = "sha256-c8FirHc+J5Y439g0BdHxRtXVrOAzIrGEKA0m1mp9b/U=";

      };

      installPhase = ''

        cp -r $src $out

      '';

    };

    run-nextflow-pipeline = pkgs.writeShellApplication {

      name = "run-nextflow-pipeline";

      runtimeInputs = [ pkgs.nextflow ];

      text = ''

        export NXF_OFFLINE=true

        for b in false true; do

          echo "docker.enabled = $b" > nextflow.config

          cat nextflow.config

          nextflow run -ansi-log false ${hello}

        done

      '';

    };

  in

  {

    name = "nextflow";

    nodes.machine =

      { ... }:

      {

        environment.systemPackages = [

          run-nextflow-pipeline

          pkgs.nextflow

        ];

        virtualisation = {

          docker.enable = true;

        };

      };

    testScript =

      { nodes, ... }:

      ''

        start_all()

        machine.wait_for_unit("docker.service")

        machine.succeed("docker load < ${bash}")

        machine.succeed("run-nextflow-pipeline >&2")

      '';

  }

)

{ lib

, stdenv

, fetchurl

, makeWrapper

, openjdk17

, wget

, which

, gnused

, gawk

, coreutils

, buildFHSEnv

{

  lib,

  stdenv,

  fetchFromGitHub,

  makeWrapper,

  openjdk,

  gradle,

  wget,

  which,

  gnused,

  gawk,

  coreutils,

  bash,

  testers,

  nixosTests,

}:

let

  nextflow =

stdenv.mkDerivation rec {

stdenv.mkDerivation (finalAttrs: {

  pname = "nextflow";

  version = "22.10.6";

  # 24.08.0-edge is compatible with Java 21. The current (as of 2024-09-19)

  # nextflow release (24.04.4) does not yet support java21, but java19. The

  # latter is not in nixpkgs(-unstable) anymore.

  version = "24.08.0-edge";

  src = fetchurl {

    url = "https://github.com/nextflow-io/nextflow/releases/download/v${version}/nextflow-${version}-all";

    hash = "sha256-zeYsKxWRnzr0W6CD+yjoAXwCN/AbN5P4HhH1oftnrjY=";

  src = fetchFromGitHub {

    owner = "nextflow-io";

    repo = "nextflow";

    rev = "6e866ae81ff3bf8a9729e9dbaa9dd89afcb81a4b";

    hash = "sha256-SA27cuP3iO5kD6u0uTeEaydyqbyJzOkVtPrb++m3Tv0=";

  };

  nativeBuildInputs = [

    makeWrapper

    openjdk17

    wget

    which

    gnused

    gawk

    coreutils

    gradle

  ];

  dontUnpack = true;

  postPatch = ''

    # Nextflow invokes the constant "/bin/bash" (not as a shebang) at

    # several locations so we fix that globally. However, when running inside

    # a container, we actually *want* "/bin/bash". Thus the global fix needs

    # to be reverted for this specific use case.

    substituteInPlace modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy \

      --replace-fail "['/bin/bash'," "['${bash}/bin/bash'," \

      --replace-fail "if( containerBuilder ) {" "if( containerBuilder ) {

                launcher = launcher.replaceFirst(\"/nix/store/.*/bin/bash\", \"/bin/bash\")"

  '';

  mitmCache = gradle.fetchDeps {

    inherit (finalAttrs) pname;

    data = ./deps.json;

  };

  __darwinAllowLocalNetworking = true;

  # During the build, some additional dependencies are downloaded ("detached

  # configuration"). We thus need to run a full build on instead of the default

  # one.

  # See https://github.com/NixOS/nixpkgs/pull/339197#discussion_r1747749061

  gradleUpdateTask = "pack";

  # The installer attempts to copy a final JAR to $HOME/.nextflow/...

  gradleFlags = ["-Duser.home=\$TMPDIR"];

  preBuild = ''

    # See Makefile (`make pack`)

    export BUILD_PACK=1

  '';

  gradleBuildTask = "pack";

  installPhase = ''

    runHook preInstall

    mkdir -p $out/bin

    install -Dm755 $src $out/bin/nextflow

    install -Dm755 build/releases/nextflow-${finalAttrs.version}-dist $out/bin/nextflow

    runHook postInstall

  '';

  postFixup = ''

    wrapProgram $out/bin/nextflow \

      --prefix PATH : ${lib.makeBinPath nativeBuildInputs} \

      --set JAVA_HOME ${openjdk17.home}

      --prefix PATH : ${

        lib.makeBinPath [

          coreutils

          gawk

          gnused

          wget

          which

        ]

      } \

      --set JAVA_HOME ${openjdk.home}

  '';

  passthru.tests.default = nixosTests.nextflow;

  # versionCheckHook doesn't work as of 2024-09-23.

  # See https://github.com/NixOS/nixpkgs/pull/339197#issuecomment-2363495060

  passthru.tests.version = testers.testVersion {

    package = finalAttrs.finalPackage;

    command = "env HOME=$TMPDIR nextflow -version";

  };

  meta = with lib; {

    description = "DSL for data-driven computational pipelines";

    longDescription = ''

    homepage = "https://www.nextflow.io/";

    changelog = "https://github.com/nextflow-io/nextflow/releases";

    license = licenses.asl20;

    maintainers = with maintainers; [ Etjean edmundmiller ];

    maintainers = with maintainers; [

      Etjean

      edmundmiller

    ];

    mainProgram = "nextflow";

    platforms = platforms.unix;

  };

};

in

if stdenv.hostPlatform.isLinux then

  buildFHSEnv

  {

    name = "nextflow";

    targetPkgs = pkgs: [ nextflow ];

    runScript = "nextflow";

  }

else nextflow

})