depot/third_party/nixpkgs/pkgs/applications/science/biology/plink-ng/default.nix

{ lib, stdenv, fetchFromGitHub, zlib, blas, lapack, darwin}:

stdenv.mkDerivation rec {
  pname = "plink-ng";
  version = "1.90b3";

  src = fetchFromGitHub {
    owner = "chrchang";
    repo = "plink-ng";
    rev = "v${version}";
    sha256 = "1zhffjbwpd50dxywccbnv1rxy9njwz73l4awc5j7i28rgj3davcq";
  };

  buildInputs = [ zlib ] ++ (if stdenv.isDarwin then [ darwin.apple_sdk.frameworks.Accelerate ] else [ blas lapack ]) ;

  preBuild = ''
    sed -i 's|zlib-1.2.8/zlib.h|zlib.h|g' *.c *.h
    ${lib.optionalString stdenv.cc.isClang "sed -i 's|g++|clang++|g' Makefile.std"}

    makeFlagsArray+=(
      ZLIB=-lz
      BLASFLAGS="-lblas -lcblas -llapack"
    );
  '';

  makefile = "Makefile.std";

  installPhase = ''
    mkdir -p $out/bin
    cp plink $out/bin
  '';

  meta = {
    broken = (stdenv.isLinux && stdenv.isAarch64);
    description = "A comprehensive update to the PLINK association analysis toolset";
    mainProgram = "plink";
    homepage = "https://www.cog-genomics.org/plink2";
    license = lib.licenses.gpl3;
    platforms = lib.platforms.linux;
  };
}