pkgs/by-name/sp/spades/package.nix

   1 {
   2   lib,
   3   stdenv,
   4   bzip2,
   5   cmake,
   6   fetchFromGitHub,
   7   fetchpatch,
   8   ncurses,
   9   python3,
  10   readline,
  11 }:
  12
  13 stdenv.mkDerivation (finalAttrs: {
  14   pname = "spades";
  15   version = "4.0.0";
  16
  17   src = fetchFromGitHub {
  18     owner = "ablab";
  19     repo = "spades";
  20     rev = "v${finalAttrs.version}";
  21     hash = "sha256-k2+ddJIgGE41KGZODovU9VdurbWerEtdqNrFDwyuFjo=";
  22   };
  23
  24   sourceRoot = "${finalAttrs.src.name}/src";
  25
  26   patches = [
  27     # https://github.com/ablab/spades/pull/1314
  28     (fetchpatch {
  29       name = "copytree.patch";
  30       url = "https://github.com/ablab/spades/commit/af1f756a46c5da669897b841d4f753af1eaa9588.patch";
  31       hash = "sha256-tkT7hb0TqsbLkcTs9u43nzvV8bVdh3G9VKYqFFLrQv8=";
  32       stripLen = 3;
  33       extraPrefix = "projects/";
  34     })
  35   ];
  36
  37   cmakeFlags = [
  38     "-DZLIB_ENABLE_TESTS=OFF"
  39     "-DSPADES_BUILD_INTERNAL=OFF"
  40   ];
  41
  42   preConfigure = ''
  43     # The CMakeListsInternal.txt file should be empty in the release tarball
  44     echo "" > CMakeListsInternal.txt
  45   '';
  46
  47   nativeBuildInputs = [ cmake ];
  48
  49   buildInputs = [
  50     bzip2
  51     ncurses
  52     python3
  53     readline
  54   ];
  55
  56   env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.hostPlatform.isDarwin "-faligned-allocation";
  57
  58   doCheck = true;
  59
  60   strictDeps = true;
  61
  62   meta = {
  63     description = "St. Petersburg genome assembler, a toolkit for assembling and analyzing sequencing data";
  64     changelog = "https://github.com/ablab/spades/blob/${finalAttrs.version}/changelog.md";
  65     downloadPage = "https://github.com/ablab/spades";
  66     homepage = "http://ablab.github.io/spades";
  67     license = lib.licenses.gpl2Only;
  68     platforms = lib.platforms.unix;
  69     maintainers = with lib.maintainers; [ bzizou ];
  70     broken = stdenv.hostPlatform.isMusl;
  71   };
  72 })