octopus-caller: fix `gcc-13` build failure (drop `-Werror`)

Without the change the build on `master` fails as
https://hydra.nixos.org/build/249090788:

    /build/source/src/config/option_collation.cpp: In function 'auto octopus::options::make_variant_generator_builder(const OptionMap&, boost::optional<const octopus::ReadSetProfile&>)':
    /build/source/src/config/option_collation.cpp:1298: error: redundant move in initialization [-Werror=redundant-move]
     1298 |                 throw ConflictingSourceVariantFile {std::move(source_path), *output_path};
          |

Blanket `-Werror` frequently causes build failures unless upstream is
quick at addressing build failures.

1 files changed, 11 insertions, 4 deletions

diff --git a/pkgs/applications/science/biology/octopus/default.nix b/pkgs/applications/science/biology/octopus/default.nix
index 35898aae9f3e..0090ca82d6c3 100644
--- a/pkgs/applications/science/biology/octopus/default.nix
+++ b/pkgs/applications/science/biology/octopus/default.nix
@@ -19,10 +19,17 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-VaUr63v7mzhh4VBghH7a7qrqOYwl6vucmmKzTi9yAjY=";
   }) ];
 
-  env.NIX_CFLAGS_COMPILE = toString [
-    # Needed with GCC 12
-    "-Wno-error=deprecated-declarations"
-  ];
+  postPatch = ''
+    # Disable -Werror to avoid build failure on fresh toolchains like
+    # gcc-13.
+    substituteInPlace lib/date/CMakeLists.txt --replace-fail ' -Werror ' ' '
+    substituteInPlace lib/ranger/CMakeLists.txt --replace-fail ' -Werror ' ' '
+    substituteInPlace lib/tandem/CMakeLists.txt --replace-fail ' -Werror ' ' '
+    substituteInPlace src/CMakeLists.txt --replace-fail ' -Werror ' ' '
+
+    # Fix gcc-13 build due to missing <cstdint> header.
+    sed -e '1i #include <cstdint>' -i src/core/tools/vargen/utils/assembler.hpp
+  '';
 
   postInstall = ''
     mkdir $out/bin