From 90a5d1b931d48ce9764c541d06bc57848b2f7b9e Mon Sep 17 00:00:00 2001
From: Sergei Trofimovich <slyich@gmail.com>
Date: Sat, 10 Feb 2024 10:26:43 +0000
Subject: [PATCH] megahit: fir `gcc-13` build failure

Without the change build fails on `master` against `gcc-13` as
https://hydra.nixos.org/build/247673319:

    In file included from /build/source/src/main_local_assemble.cpp:27:
    /build/source/src/localasm/local_assemble.h:31:3: error: 'uint32_t' does not name a type
       31 |   uint32_t kmin{11};
          |   ^~~~~~~~
    /build/source/src/localasm/local_assemble.h:1:1: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
      +++ |+#include <cstdint>
---
 .../applications/science/biology/megahit/default.nix | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/pkgs/applications/science/biology/megahit/default.nix b/pkgs/applications/science/biology/megahit/default.nix
index 7f054a51d5e0..5fa9420bc87c 100644
--- a/pkgs/applications/science/biology/megahit/default.nix
+++ b/pkgs/applications/science/biology/megahit/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, cmake, zlib }:
+{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, zlib }:
 
 stdenv.mkDerivation rec {
   pname    = "megahit";
@@ -11,6 +11,16 @@ stdenv.mkDerivation rec {
     sha256 = "1r5d9nkdmgjsbrpj43q9hy3s8jwsabaz3ji561v18hy47v58923c";
   };
 
+  patches = [
+    # Fix gcc-13 build failure:
+    #   https://github.com/voutcn/megahit/pull/366
+    (fetchpatch {
+      name = "gcc-13.patch";
+      url = "https://github.com/voutcn/megahit/commit/4cb2f793503087163bda8592222f105f27e33e66.patch";
+      hash = "sha256-b5mhzif+OPcMjmg+BnaUc5CB6Acn/KTBOJEw+WYEhbs=";
+    })
+  ];
+
   nativeBuildInputs = [ cmake ];
   buildInputs = [ zlib ];