{ stdenv, fetchurl
, bash }:

stdenv.mkDerivation rec {
  version = "1.1.3";
  name = "idba-${version}";

  src = fetchurl {
    url = "https://github.com/loneknightpy/idba/releases/download/${version}/idba-${version}.tar.gz";
    sha256 = "1l16mvxyr226gzrd0kw423im2nv07dvvzaib40f5qwkd7i3283h3";
  };

  # increase max sequence length to 256 
  postPatch = ''
    sed -i 's/kMaxShortSequence = 128/kMaxShortSequence = 256/' src/sequence/short_sequence.h
  '';

  # default 'make install' has a bug that doesn't install all the binaries
  installPhase = ''
    mkdir -p $out/bin
    find ./bin -maxdepth 1 -type f -perm /a+x -exec cp -av {} $out/bin \;
  '';

  # buildInputs = [
  #   stdenv
  # ];

  meta = with stdenv.lib; {
    homepage = https://github.com/loneknightpy/idba/;
    description = "Basic iterative de Bruijn graph assembler for second-generation sequencing reads";
    longDescription = "IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth regions and use progressive depth on contigs to reduce errors in high-depth regions. It is a generic purpose assembler and especially good for single-cell and metagenomic sequencing data. IDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference genome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for RNA-Seq data.";
    platforms = platforms.all;
    license = licenses.gpl3;
  };

  enableParallelBuilding = true;
}