Merge pull request #307399 from natsukium/mafft/update

{ lib, stdenv, fetchFromGitLab }:

{

  lib,

  stdenv,

  fetchFromGitLab,

  runCommand,

  mafft,

}:

stdenv.mkDerivation rec {

stdenv.mkDerivation (finalAttrs: {

  pname = "mafft";

  version = "7.525";

  version = "7.526";

  src = fetchFromGitLab {

    owner = "sysimm";

    repo = pname;

    rev = "v${version}";

    sha256 = "sha256-ckBmvFssYAmYcBHAEftjQqBV0MB0theGfemaPx3XUws=";

    repo = "mafft";

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

    hash = "sha256-VNe00r12qEkLEbpZdJCe5xZ73JA3uAmuAeG+eSeRDI0=";

  };

  preBuild = ''

    make clean

  '';

  makeFlags = [ "CC=${stdenv.cc.targetPrefix}cc" "PREFIX=$(out)" ];

  makeFlags = [

    "CC=${stdenv.cc.targetPrefix}cc"

    "PREFIX=$(out)"

  ];

  meta = with lib;

    {

  passthru.tests = {

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

      mkdir $out

      cd ${finalAttrs.src}/test

      ${lib.getExe mafft} sample > $out/test.fftns2

      ${lib.getExe mafft} --maxiterate 100  sample > $out/test.fftnsi

      ${lib.getExe mafft} --globalpair sample > $out/test.gins1

      ${lib.getExe mafft} --globalpair --maxiterate 100  sample > $out/test.ginsi

      ${lib.getExe mafft} --localpair sample > $out/test.lins1

      ${lib.getExe mafft} --localpair --maxiterate 100  sample > $out/test.linsi

      diff $out/test.fftns2 sample.fftns2

      diff $out/test.fftnsi sample.fftnsi

      diff $out/test.gins1 sample.gins1

      diff $out/test.ginsi sample.ginsi

      diff $out/test.lins1 sample.lins1

    '';

  };

  meta = with lib; {

    description = "Multiple alignment program for amino acid or nucleotide sequences";

    homepage = "https://mafft.cbrc.jp/alignment/software/";

    license = licenses.bsd3;

    maintainers = with maintainers; [ natsukium ];

    platforms = platforms.unix;

  };

}

})