From b02006abd1e4e11c8d05812089618dae10c19c52 Mon Sep 17 00:00:00 2001
From: coolcuber <rpgeorg@clemson.edu>
Date: Tue, 28 Jul 2026 19:35:03 -0400
Subject: [PATCH] bwa-mem2: unstable-2023-03-18->2.3, add versionCheckHook

---
 pkgs/by-name/bw/bwa-mem2/package.nix | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/pkgs/by-name/bw/bwa-mem2/package.nix b/pkgs/by-name/bw/bwa-mem2/package.nix
index 7ce7e218bbf0..9fe8c0a87bf6 100644
--- a/pkgs/by-name/bw/bwa-mem2/package.nix
+++ b/pkgs/by-name/bw/bwa-mem2/package.nix
@@ -3,18 +3,19 @@
   stdenv,
   fetchFromGitHub,
   safestringlib,
+  versionCheckHook,
   zlib,
 }:
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "bwa-mem2";
-  version = "unstable-2023-03-18";
+  version = "2.3";
 
   src = fetchFromGitHub {
     owner = "bwa-mem2";
     repo = "bwa-mem2";
-    rev = "cf4306a47dac35e7e79a9e75398a35f33900cfd0";
-    hash = "sha256-hY8nLRFWt0GAElhDIcYdUX6cJrzOE3NlYRQr0tC3on4=";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-DBgAX18YwXbBxUlHHCDeiYJ6fcuVzLZ2ZrEta5zPsAU=";
   };
 
   buildInputs = [ zlib ];
@@ -82,6 +83,13 @@ stdenv.mkDerivation (finalAttrs: {
     runHook postInstall
   '';
 
+  # TODO change this when https://github.com/bwa-mem2/bwa-mem2/issues/283 gets fixed
+  doInstallCheck = false;
+
+  nativeInstallCheckInputs = [ versionCheckHook ];
+
+  versionCheckProgramArg = "version";
+
   meta = {
     description = "Next version of the bwa-mem algorithm in bwa, a software package for mapping low-divergent sequences against a large reference genome";
     mainProgram = "bwa-mem2";