From 6e99fa330520ef8398480b28f8b92ebb0d0eea59 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Thu, 29 May 2025 00:26:26 +0000
Subject: [PATCH] rtg-tools: 3.12.1 -> 3.13

Fix jdk path.
---
 pkgs/by-name/rt/rtg-tools/package.nix | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/pkgs/by-name/rt/rtg-tools/package.nix b/pkgs/by-name/rt/rtg-tools/package.nix
index d61c7f288415..2667bdc92663 100644
--- a/pkgs/by-name/rt/rtg-tools/package.nix
+++ b/pkgs/by-name/rt/rtg-tools/package.nix
@@ -13,13 +13,13 @@
 
 stdenv.mkDerivation rec {
   pname = "rtg-tools";
-  version = "3.12.1";
+  version = "3.13";
 
   src = fetchFromGitHub {
     owner = "RealTimeGenomics";
     repo = "rtg-tools";
     rev = version;
-    hash = "sha256-fMrrjrgaGxBVxn6qMq2g0oFv6qtfhZcQlkvv1E9Os6Y=";
+    hash = "sha256-vPzKrgnX6BCQmn9aOVWWpFLC6SbPBHZhZ+oL1LCbvmo=";
   };
 
   nativeBuildInputs = [
@@ -47,12 +47,11 @@ stdenv.mkDerivation rec {
     # Use a location outside nix (must be writable)
     substituteInPlace installer/rtg \
       --replace-fail  '$THIS_DIR/rtg.cfg' '$HOME/.config/rtg-tools/rtg.cfg'  \
-      --replace-fail 'RTG_JAVA="java"' 'RTG_JAVA="${jdk}/lib/opendk/bin/java"' \
+       --replace-fail 'RTG_JAVA="java"' 'RTG_JAVA="${lib.getExe jdk}"' \
       --replace-fail uname ${lib.getExe' coreutils "uname"} \
       --replace-fail awk ${lib.getExe gawk} \
       --replace-fail "hostname -s" "${lib.getExe hostname} -s"
 
-
     sed -i '/USER_JAVA_OPTS=$RTG_JAVA_OPTS/a mkdir -p $HOME/.config/rtg-tools'  installer/rtg
   '';