From 3ec130156ecc251cc64a77bf050b184fbc38bedd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Th=C3=A9o=20Bori?= <theobori@disroot.org>
Date: Tue, 28 Apr 2026 21:40:38 +0200
Subject: [PATCH] phylophlan: cleanup the nix declaration

---
 pkgs/by-name/ph/phylophlan/package.nix | 97 +++++++++++++-------------
 1 file changed, 50 insertions(+), 47 deletions(-)

diff --git a/pkgs/by-name/ph/phylophlan/package.nix b/pkgs/by-name/ph/phylophlan/package.nix
index 78b307e46972..729c93d9fcbf 100644
--- a/pkgs/by-name/ph/phylophlan/package.nix
+++ b/pkgs/by-name/ph/phylophlan/package.nix
@@ -8,60 +8,63 @@
   diamond,
   python3Packages,
 }:
-let
-  finalAttrs = {
-    pname = "phylophlan";
-    version = "3.2.1";
-    pyproject = true;
 
-    src = fetchFromGitHub {
-      owner = "biobakery";
-      repo = "phylophlan";
-      tag = finalAttrs.version;
-      hash = "sha256-rPTEdu0W3LD27tDIWCOQ3K+RJuj97I9aEeYFdM77jOs=";
-    };
+python3Packages.buildPythonApplication (finalAttrs: {
+  pname = "phylophlan";
+  version = "3.2.1";
+  pyproject = true;
 
-    build-system = with python3Packages; [ setuptools ];
+  src = fetchFromGitHub {
+    owner = "biobakery";
+    repo = "phylophlan";
+    tag = finalAttrs.version;
+    hash = "sha256-rPTEdu0W3LD27tDIWCOQ3K+RJuj97I9aEeYFdM77jOs=";
+  };
 
-    # It has no tests
-    doCheck = false;
+  build-system = with python3Packages; [ setuptools ];
 
-    dependencies = with python3Packages; [
-      biopython
-      dendropy
-      matplotlib
-      numpy
-      pandas
-      seaborn
-      distutils
-      requests
-      scipy
-      tqdm
-    ];
+  # It has no tests
+  doCheck = false;
 
+  dependencies = with python3Packages; [
+    biopython
+    dendropy
+    matplotlib
+    numpy
+    pandas
+    seaborn
+    distutils
+    requests
+    scipy
+    tqdm
+  ];
+
+  preFixup = ''
     # Minimum needed external tools
     # See https://github.com/biobakery/phylophlan/wiki#dependencies
-    propagatedBuildInputs = [
-      raxml
-      mafft
-      trimal
-      blast
-      diamond
-    ];
+    makeWrapperArgs+=(--prefix PATH : ${
+      lib.makeBinPath [
+        raxml
+        mafft
+        trimal
+        blast
+        diamond
+      ]
+    }
+    )
+  '';
 
-    postInstall = ''
-      # Not revelant in this context
-      rm -f $out/bin/phylophlan_write_default_configs.sh
-    '';
+  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";
-    };
+  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
+})