Merge pull request #231635 from natsukium/bwa/build-on-aarch64

{ lib, stdenv, fetchurl, fetchpatch, zlib }:

{ lib, stdenv, fetchFromGitHub, zlib }:

stdenv.mkDerivation rec {

stdenv.mkDerivation {

  pname = "bwa";

  version = "0.7.17";

  version = "unstable-2022-09-23";

  src = fetchurl {

    url = "mirror://sourceforge/bio-bwa/${pname}-${version}.tar.bz2";

    sha256 = "1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy";

  src = fetchFromGitHub {

    owner = "lh3";

    repo = "bwa";

    rev = "139f68fc4c3747813783a488aef2adc86626b01b";

    hash = "sha256-8u35lTK6gBKeapYoIkG9MuJ/pyy/HFA2OiPn+Ml2C6c=";

  };

  patches = [

    # Pull upstream patch for -fno-common toolchain support like upstream

    # gcc-10: https://github.com/lh3/bwa/pull/267

    (fetchpatch {

      name  = "fno-common.patch";

      url = "https://github.com/lh3/bwa/commit/2a1ae7b6f34a96ea25be007ac9d91e57e9d32284.patch";

      sha256 = "1lihfxai6vcshv5vr3m7yhk833bdivkja3gld6ilwrc4z28f6wqy";

    })

  ];

  buildInputs = [ zlib ];

  # Avoid hardcoding gcc to allow environments with a different

  # it's unclear which headers are intended to be part of the public interface

  # so we may find ourselves having to add more here over time

  installPhase = ''

    runHook preInstall

    install -vD -t $out/bin bwa

    install -vD -t $out/lib libbwa.a

    install -vD -t $out/include bntseq.h

    install -vD -t $out/include bwa.h

    install -vD -t $out/include bwamem.h

    install -vD -t $out/include bwt.h

    runHook postInstall

  '';

  meta = with lib; {

    description = "A software package for mapping low-divergent sequences against a large reference genome, such as the human genome";

    license     = licenses.gpl3;

    license     = licenses.gpl3Plus;

    homepage    = "https://bio-bwa.sourceforge.net/";

    maintainers = with maintainers; [ luispedro ];

    platforms = platforms.x86_64;

    platforms = platforms.unix;

  };

}