From 2ce78bd571a7985f40024af2d4ac2aa407c3e383 Mon Sep 17 00:00:00 2001
From: Alexis Praga <alexis.praga@gmail.com>
Date: Fri, 16 Sep 2022 21:43:51 +0200
Subject: [PATCH] gatk: add java and python to PATH

gatk is actually a python script that starts either the local or spark
.jar file according to a fixed setup.
In the initial commit, neither java nor python were present in PATH.
---
 pkgs/applications/science/biology/gatk/default.nix | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/science/biology/gatk/default.nix b/pkgs/applications/science/biology/gatk/default.nix
index c0818b8336df..9853b0322c01 100644
--- a/pkgs/applications/science/biology/gatk/default.nix
+++ b/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; {