phylophlan: init at 3.1.1 (#356788)

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

@@ -0,0 +1,65 @@
+{
+  lib,
+  fetchFromGitHub,
+  raxml,
+  mafft,
+  trimal,
+  blast,
+  diamond,
+  python3Packages,
+}:
+let
+  finalAttrs = {
+    pname = "phylophlan";
+    version = "3.1.1";
+    pyproject = true;
+
+    src = fetchFromGitHub {
+      owner = "biobakery";
+      repo = "phylophlan";
+      rev = "refs/tags/${finalAttrs.version}";
+      hash = "sha256-KlWKt2tH2lQBh/eQ2Hbcu2gXHEFfmFEc6LrybluxINc=";
+    };
+
+    build-system = with python3Packages; [ setuptools ];
+
+    # It has no tests
+    doCheck = false;
+
+    dependencies = with python3Packages; [
+      biopython
+      dendropy
+      matplotlib
+      numpy
+      pandas
+      seaborn
+      distutils
+      requests
+    ];
+
+    # Minimum needed external tools
+    # See https://github.com/biobakery/phylophlan/wiki#dependencies
+    propagatedBuildInputs = [
+      raxml
+      mafft
+      trimal
+      blast
+      diamond
+    ];
+
+    postInstall = ''
+      # Not revelant in this context
+      rm -f $out/bin/phylophlan_write_default_configs.sh
+    '';
+
+    meta = {
+      homepage = "https://github.com/biobakery/phylophlan";
+      description = "Precise phylogenetic analysis of microbial isolates and genomes from metagenomes";
+      changelog = "https://github.com/biobakery/phylophlan/releases";
+      license = lib.licenses.mit;
+      maintainers = with lib.maintainers; [ theobori ];
+      mainProgram = "phylophlan";
+    };
+  };
+in
+python3Packages.buildPythonApplication finalAttrs