Merge pull request #243431 from natsukium/kssd/update

{ lib, stdenv, fetchFromGitHub, fetchpatch, zlib, automake, autoconf, libtool }:

{ lib

, stdenv

, fetchFromGitHub

, fetchpatch

, zlib

, kssd

, runCommand

}:

stdenv.mkDerivation rec {

stdenv.mkDerivation (finalAttrs: {

  pname = "kssd";

  version = "1.1";

  version = "2.21";

  src = fetchFromGitHub {

    owner = "yhg926";

    repo = "public_kssd";

    rev = "v${version}";

    sha256 = "sha256-8jzYqo9LXF66pQ1EIusm+gba2VbTYpJz2K3NVlA3QxY=";

    rev = "v${finalAttrs.version}";

    hash = "sha256-D/s1jL2oKE0rSdRMVljskYFsw5UPOv1L95Of+K+e17w=";

  };

  patches = [

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

    #   https://github.com/yhg926/public_kssd/pull/9

    # https://github.com/yhg926/public_kssd/pull/11

    (fetchpatch {

      name = "fno-common.patch";

      url = "https://github.com/yhg926/public_kssd/commit/cdd1e8aae256146f5913a3b4c723b638d53bdf27.patch";

      sha256 = "sha256-HhaTRqPfKR+ouh0PwEH6u22pbuqbX2OypRzw8BXm0W4=";

      name = "allocate-enough-memory.patch";

      url = "https://github.com/yhg926/public_kssd/commit/b1e66bbcc04687bc3201301cd742a0b26a87cb5d.patch";

      hash = "sha256-yFyJetpsGKeu+H6Oxrmn5ea4ESVtblb3YJDja4JEAEM=";

    })

  ];

  nativeBuildInputs = [ autoconf automake ];

  buildInputs = [ zlib libtool ];

  buildInputs = [ zlib ];

  installPhase = ''

    runHook preInstall

    install -vD kssd $out/bin/kssd

    runHook postInstall

  '';

  passthru.tests = {

    simple = runCommand "${finalAttrs.pname}-test" { } ''

      mkdir $out

      ${lib.getExe kssd} dist -L ${kssd.src}/shuf_file/L3K10.shuf -r ${kssd.src}/test_fna/seqs1 -o $out/reference

      ${lib.getExe kssd} dist -L ${kssd.src}/shuf_file/L3K10.shuf -o $out/query ${kssd.src}/test_fna/seqs2

      ${lib.getExe kssd} dist -r $out/reference -o $out/distout $out/query

    '';

  };

  meta = with lib; {

    description = "K-mer substring space decomposition";

    license     = licenses.asl20;

    homepage    = "https://github.com/yhg926/public_kssd";

    maintainers = with maintainers; [ unode ];

    platforms = [ "x86_64-linux" ];

    platforms = platforms.linux;

    mainProgram = "kssd";

  };

}

})