Commit 5db72db7 authored by Alexis Praga's avatar Alexis Praga
Browse files

hap-py: use rtgtools vcfeval as default core 

For best results (quality and running time), the
authors advice to use RTGtools vcfeval as the
engine.

Depends on #230394
parent 946f357e

pkgs/by-name/ha/hap-py/package.nix

+50 −19
Original line number Diff line number Diff line 
{ pkgs, stdenv, fetchFromGitHub, boost, zlib, lib, makeWrapper }:

{

  autoconf,

  bcftools,

  boost,

  bzip2,

  cmake,

  curl,

  fetchFromGitHub,

  htslib,

  lib,

  makeWrapper,

  perl,

  python3,

  rtg-tools,

  samtools,

  stdenv,

  xz,

  zlib,

}:



let

  # Bcftools needs perl

  runtime = with pkgs; [ bcftools htslib my-python perl samtools ];

  my-python-packages = p: with p; [

  runtime =  [

    bcftools

    htslib

    my-python

    perl

    samtools

  ];

  my-python-packages =

    p: with p; [

      bx-python

      pysam

    cython

      pandas

      psutil

    nose

      scipy

    ];

  my-python = pkgs.python3.withPackages my-python-packages;

  my-python = python3.withPackages my-python-packages;

in

stdenv.mkDerivation rec {

  pname = "hap.py";

  version = "0.3.15";



  src = fetchFromGitHub {

    owner = "Illumina";

    repo = pname;
@@ -29,26 +53,33 @@ stdenv.mkDerivation rec { 
  # For cmake : boost lib and includedir are in differernt location

  BOOST_LIBRARYDIR = "${boost.out}/lib";

  BOOST_INCLUDEDIR = "${boost.dev}/include";



  patches = [

    ./hap-py.patch

    ./cmake.patch

    # Compatibility with nix for boost and library flags : zlib, bzip2, curl, crypto, lzma

    ./boost-library-flags.patch

    # Update to python3

    ./python3.patch

  ];

  buildInputs = with pkgs; [

  nativeBuildInputs = [

    autoconf

    cmake

    makeWrapper

  ];

  buildInputs = [

    boost

    bzip2

    cmake

    curl

    htslib

    my-python

    rtg-tools

    xz

    zlib

  ];

  nativeBuildInputs = [ pkgs.makeWrapper ];

  propagatedBuildInputs = runtime;



  postFixup = ''

    wrapProgram $out/bin/hap.py \

      --set PATH ${lib.makeBinPath runtime}

       --set PATH ${lib.makeBinPath runtime} \

       --add-flags "--engine-vcfeval-path=${rtg-tools}/bin/rtg"

  '';



  meta = with lib; {