{ stdenv, fetchFromGitHub
, jdk, ant, makeWrapper
, jre, perl }:

stdenv.mkDerivation rec {
  name = "FastQC-${version}";
  version = "0.11.8";
  src = fetchFromGitHub {
    name = "${name}-src";
    owner = "s-andrews";
    repo = "FastQC";
    rev = "v${version}";
    sha256 = "1xyf54ylvpv9kp110sf0hp1lqzx8plxh7a0k5yipggyqqhviv77j";
  };

  buildInputs = [ perl jdk ant makeWrapper ];

  buildPhase = "ant";

  installPhase = ''
    install -d $out/share/FastQC $out/bin
    install bin/fastqc $out/share/FastQC
    cp -r bin/{Configuration,Help,Templates} $out/share/FastQC/
    cp -r bin/{net,org,uk} $out/share/FastQC/
    makeWrapper $out/share/FastQC/fastqc $out/bin/fastqc --add-flags --java=${jre}/bin/java
  '';

  meta = with stdenv.lib; {
    homepage = https://www.bioinformatics.babraham.ac.uk/projects/fastqc/;
    description = "A quality control tool 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.
    '';
    platforms = platforms.all;
    license = licenses.gpl2Plus;
  };
}