hap-py: cleanup, fix cmake 4 compatibility (#468825)

pkgs/by-name/ha/hap-py/package.nix

@@ -37,22 +37,26 @@ let
     ];
   my-python = python3.withPackages my-python-packages;
 in
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "hap.py";
   version = "0.3.15";
 
   src = fetchFromGitHub {
     owner = "Illumina";
     repo = "hap.py";
-    rev = "v${version}";
+    tag = "v${finalAttrs.version}";
     hash = "sha256-K8XXhioMGMHw56MKvp0Eo8S6R36JczBzGRaBz035zRQ=";
   };
-  # For illumina script
-  BOOST_ROOT = "${boost.out}";
-  ZLIBSTATIC = "${zlib.static}";
-  # For cmake : boost lib and includedir are in different location
-  BOOST_LIBRARYDIR = "${boost.out}/lib";
-  BOOST_INCLUDEDIR = "${boost.dev}/include";
+
+  # CMake 4 dropped support of versions lower than 3.5,
+  # versions lower than 3.10 are deprecated.
+  # https://github.com/NixOS/nixpkgs/issues/445447
+  postPatch = ''
+    substituteInPlace CMakeLists.txt \
+      --replace-fail \
+        "cmake_minimum_required (VERSION 2.8)" \
+        "cmake_minimum_required (VERSION 3.10)"
+  '';
 
   patches = [
     # Compatibility with nix for boost and library flags : zlib, bzip2, curl, crypto, lzma
@@ -76,17 +80,27 @@ stdenv.mkDerivation rec {
     zlib
   ];
 
+  env = {
+    # For illumina script
+    BOOST_ROOT = "${boost.out}";
+    ZLIBSTATIC = "${zlib.static}";
+
+    # For cmake : boost lib and includedir are in different location
+    BOOST_LIBRARYDIR = "${boost.out}/lib";
+    BOOST_INCLUDEDIR = "${boost.dev}/include";
+  };
+
   postFixup = ''
     wrapProgram $out/bin/hap.py \
        --set PATH ${lib.makeBinPath runtime} \
-       --add-flags "--engine-vcfeval-path=${rtg-tools}/bin/rtg"
+       --add-flags "--engine-vcfeval-path=${lib.getExe rtg-tools}"
   '';
 
-  meta = with lib; {
+  meta = {
     description = "Compare genetics variants against a gold dataset";
     homepage = "https://github.com/Illumina/hap.py";
-    license = licenses.bsd2;
-    maintainers = with maintainers; [ apraga ];
+    license = lib.licenses.bsd2;
+    maintainers = with lib.maintainers; [ apraga ];
     mainProgram = "hap.py";
   };
-}
+})

pkgs/by-name/rt/rtg-tools/package.nix

@@ -11,14 +11,14 @@
   unzip,
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "rtg-tools";
   version = "3.13";
 
   src = fetchFromGitHub {
     owner = "RealTimeGenomics";
     repo = "rtg-tools";
-    rev = version;
+    rev = finalAttrs.version;
     hash = "sha256-vPzKrgnX6BCQmn9aOVWWpFLC6SbPBHZhZ+oL1LCbvmo=";
   };
 
@@ -59,11 +59,12 @@ stdenv.mkDerivation rec {
     ant runalltests
   '';
 
-  meta = with lib; {
+  meta = {
     homepage = "https://github.com/RealTimeGenomics/rtg-tools";
     description = "Useful utilities for dealing with VCF files and sequence data, especially vcfeval";
-    license = licenses.bsd2;
+    license = lib.licenses.bsd2;
     platforms = [ "x86_64-linux" ];
-    maintainers = with maintainers; [ apraga ];
+    maintainers = with lib.maintainers; [ apraga ];
+    mainProgram = "rtg";
   };
-}
+})