pkgs/by-name/ph/phylophlan/package.nix

   1 {
   2   lib,
   3   fetchFromGitHub,
   4   raxml,
   5   mafft,
   6   trimal,
   7   blast,
   8   diamond,
   9   python3Packages,
  10 }:
  11 let
  12   finalAttrs = {
  13     pname = "phylophlan";
  14     version = "3.1.1";
  15     pyproject = true;
  16
  17     src = fetchFromGitHub {
  18       owner = "biobakery";
  19       repo = "phylophlan";
  20       rev = "refs/tags/${finalAttrs.version}";
  21       hash = "sha256-KlWKt2tH2lQBh/eQ2Hbcu2gXHEFfmFEc6LrybluxINc=";
  22     };
  23
  24     build-system = with python3Packages; [ setuptools ];
  25
  26     # It has no tests
  27     doCheck = false;
  28
  29     dependencies = with python3Packages; [
  30       biopython
  31       dendropy
  32       matplotlib
  33       numpy
  34       pandas
  35       seaborn
  36       distutils
  37       requests
  38     ];
  39
  40     # Minimum needed external tools
  41     # See https://github.com/biobakery/phylophlan/wiki#dependencies
  42     propagatedBuildInputs = [
  43       raxml
  44       mafft
  45       trimal
  46       blast
  47       diamond
  48     ];
  49
  50     postInstall = ''
  51       # Not revelant in this context
  52       rm -f $out/bin/phylophlan_write_default_configs.sh
  53     '';
  54
  55     meta = {
  56       homepage = "https://github.com/biobakery/phylophlan";
  57       description = "Precise phylogenetic analysis of microbial isolates and genomes from metagenomes";
  58       changelog = "https://github.com/biobakery/phylophlan/releases";
  59       license = lib.licenses.mit;
  60       maintainers = with lib.maintainers; [ theobori ];
  61       mainProgram = "phylophlan";
  62     };
  63   };
  64 in
  65 python3Packages.buildPythonApplication finalAttrs