Merge pull request #191548 from apraga/gatk-patched

pkgs/applications/science/biology/gatk/default.nix

@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchzip }:
+{ lib, stdenv, fetchzip, jre, makeWrapper, python3 }:
 
 stdenv.mkDerivation rec {
   pname = "gatk";
@@ -8,10 +8,19 @@ stdenv.mkDerivation rec {
     sha256 = "0hjlsl7fxf3ankyjidqhwxc70gjh6z4lnjzw6b5fldzb0qvgfvy8";
   };
 
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ python3 ];
+
+  dontUnpack = true;
+
   installPhase = ''
     mkdir -p $out/bin
-    install -m755 -D $src/gatk $out/bin/
     install -m755 -D $src/gatk-package-${version}-local.jar $out/bin/
+    install -m755 -D $src/gatk-package-${version}-spark.jar $out/bin/
+    install -m755 -D $src/gatk $out/bin/
+  '';
+  postFixup = ''
+    wrapProgram $out/bin/gatk --prefix PATH : ${lib.makeBinPath [ jre ]}
   '';
 
   meta = with lib; {