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
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@ -1,22 +1,46 @@
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{ pkgs, stdenv, fetchFromGitHub, boost, zlib, lib, makeWrapper }:
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{
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autoconf,
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bcftools,
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boost,
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bzip2,
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cmake,
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curl,
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fetchFromGitHub,
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htslib,
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lib,
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makeWrapper,
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perl,
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python3,
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rtg-tools,
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samtools,
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stdenv,
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xz,
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zlib,
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}:
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let
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let
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# Bcftools needs perl
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# Bcftools needs perl
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runtime = with pkgs; [ bcftools htslib my-python perl samtools ];
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runtime = [
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my-python-packages = p: with p; [
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bcftools
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bx-python
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htslib
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pysam
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my-python
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cython
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perl
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pandas
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samtools
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psutil
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nose
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scipy
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];
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];
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my-python = pkgs.python3.withPackages my-python-packages;
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my-python-packages =
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p: with p; [
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bx-python
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pysam
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pandas
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psutil
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scipy
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];
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my-python = python3.withPackages my-python-packages;
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in
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in
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stdenv.mkDerivation rec {
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stdenv.mkDerivation rec {
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pname = "hap.py";
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pname = "hap.py";
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version = "0.3.15";
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version = "0.3.15";
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src = fetchFromGitHub {
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src = fetchFromGitHub {
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owner = "Illumina";
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owner = "Illumina";
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repo = pname;
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repo = pname;
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@ -29,26 +53,33 @@ stdenv.mkDerivation rec {
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# For cmake : boost lib and includedir are in differernt location
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# For cmake : boost lib and includedir are in differernt location
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BOOST_LIBRARYDIR = "${boost.out}/lib";
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BOOST_LIBRARYDIR = "${boost.out}/lib";
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BOOST_INCLUDEDIR = "${boost.dev}/include";
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BOOST_INCLUDEDIR = "${boost.dev}/include";
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patches = [
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patches = [
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./hap-py.patch
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# Compatibility with nix for boost and library flags : zlib, bzip2, curl, crypto, lzma
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./cmake.patch
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./boost-library-flags.patch
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# Update to python3
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./python3.patch
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];
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];
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buildInputs = with pkgs; [
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nativeBuildInputs = [
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autoconf
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autoconf
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cmake
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makeWrapper
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];
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buildInputs = [
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boost
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boost
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bzip2
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bzip2
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cmake
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curl
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curl
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htslib
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htslib
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my-python
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my-python
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rtg-tools
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xz
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xz
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zlib
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zlib
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];
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];
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nativeBuildInputs = [ pkgs.makeWrapper ];
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propagatedBuildInputs = runtime;
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postFixup = ''
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postFixup = ''
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wrapProgram $out/bin/hap.py \
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wrapProgram $out/bin/hap.py \
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--set PATH ${lib.makeBinPath runtime}
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--set PATH ${lib.makeBinPath runtime} \
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--add-flags "--engine-vcfeval-path=${rtg-tools}/bin/rtg"
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'';
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'';
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meta = with lib; {
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meta = with lib; {
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