From 14a19fa225289d23b1c4f13d98e15480a25b9331 Mon Sep 17 00:00:00 2001
From: Manuel Frischknecht <manuel.frischknecht@gmail.com>
Date: Thu, 8 Feb 2024 21:54:47 +0000
Subject: [PATCH] hh-suite: fix build on GCC 13

The build of `hh-suite` stopped working with GCC 13 because
GCC stopped transitively including a couple of headers like
`cstdint` in various scenarios.

There already is an upstream PR proposed that fixes this issue [1]
but hasn't been merged yet. This change pulls in this correction
using `fetchpatch`, fixing the build for now.

[1]: https://github.com/soedinglab/hh-suite/pull/357
---
 pkgs/applications/science/biology/hh-suite/default.nix | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/pkgs/applications/science/biology/hh-suite/default.nix b/pkgs/applications/science/biology/hh-suite/default.nix
index 2e01ace7d0f1..76c6544b3430 100644
--- a/pkgs/applications/science/biology/hh-suite/default.nix
+++ b/pkgs/applications/science/biology/hh-suite/default.nix
@@ -1,6 +1,7 @@
 { lib
 , stdenv
 , fetchFromGitHub
+, fetchpatch
 , cmake
 , xxd
 , enableMpi ? false
@@ -18,6 +19,15 @@ stdenv.mkDerivation rec {
     hash = "sha256-kjNqJddioCZoh/cZL3YNplweIGopWIGzCYQOnKDqZmw=";
   };
 
+  patches = [
+    # Should be removable as soon as this upstream PR is merged: https://github.com/soedinglab/hh-suite/pull/357
+    (fetchpatch {
+      name = "fix-gcc13-build-issues.patch";
+      url = "https://github.com/soedinglab/hh-suite/commit/cec47cba5dcd580e668b1ee507c9282fbdc8e7d7.patch";
+      hash = "sha256-Msdmj9l8voPYXK0SSwUA6mEbFLBhTjjE/Kjp0VL4Kf4=";
+    })
+  ];
+
   nativeBuildInputs = [ cmake xxd ];
   cmakeFlags = lib.optional stdenv.hostPlatform.isx86 "-DHAVE_SSE2=1"
     ++ lib.optional stdenv.hostPlatform.isAarch "-DHAVE_ARM8=1"