Merge pull request #294891 from dflores1/fastqc

    github = "dfithian";

    githubId = 8409320;

  };

  dflores = {

    email = "dflores.country455@passinbox.com";

    name = "David Flores";

    github = "dflores1";

    githubId = 8538265;

  };

  dfordivam = {

    email = "dfordivam+nixpkgs@gmail.com";

    github = "dfordivam";

{ lib,

  stdenv,

  fetchzip,

  jre,

  perl,

  makeWrapper,

  imagemagick,

  makeDesktopItem,

  copyDesktopItems,

  desktopToDarwinBundle,

  testers

}:

stdenv.mkDerivation (finalAttrs: {

  pname = "fastqc";

  version = "0.12.1";

  src = fetchzip {

    url = "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v${finalAttrs.version}.zip";

    hash = "sha256-TenRG2x8ivJ2HM2ZpLaJShp0yI0Qc6K5lW5/NJFAa1I";

  };

  dontBuild = true;

  nativeBuildInputs = [ makeWrapper imagemagick ]

                      ++ lib.optional stdenv.isLinux copyDesktopItems # postInstallHook

                      ++ lib.optional stdenv.isDarwin desktopToDarwinBundle; #fixupOutputHook

  buildInputs = [ jre perl];

  desktopItem = (makeDesktopItem {

    name = "FastQC";

    exec = "fastqc";

    icon = "fastqc";

    desktopName = "FastQC";

    comment = finalAttrs.meta.description;

    categories = [ "Science" ];

  });

  desktopItems = [ finalAttrs.desktopItem ];

  installPhase = ''

    runHook preInstall

    mkdir -p $out/{bin,FastQC}

    cp -r $src/* $out/FastQC

    # Create desktop item

    mkdir -p $out/share/{applications,icons}

    # Freedesktop doesn't support windows ICO files. Use imagemagick to convert it to PNG

    convert $out/FastQC/fastqc_icon.ico $out/share/icons/fastqc.png

    runHook postInstall

  '';

  preFixup = ''

    makeWrapper $out/FastQC/fastqc $out/bin/fastqc --prefix PATH : ${jre}/bin

  '';

  passthru.tests.version = testers.testVersion {

    package = finalAttrs.finalPackage;

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

  };

  meta = {

    description = "A quality control application for high throughput sequence data";

    longDescription = ''

    FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

    The main functions of FastQC are

    - Import of data from BAM, SAM or FastQ files (any variant)

    - Providing a quick overview to tell you in which areas there may be problems

    - Summary graphs and tables to quickly assess your data

    - Export of results to an HTML based permanent report

    - Offline operation to allow automated generation of reports without running the interactive application

    '';

    homepage = "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/";

    sourceProvenance = [ lib.sourceTypes.binaryNativeCode ];

    license = with lib.licenses; [ gpl3Plus asl20 ];

    maintainers = [ lib.maintainers.dflores ];

    mainProgram = "fastqc";

    platforms = lib.platforms.unix;

  };

})