From 6f20f07dd704c4a83e8c236e51c04e2f1a05d6db Mon Sep 17 00:00:00 2001
From: Tom Hunze <dev@thunze.de>
Date: Sat, 14 Jun 2025 11:28:47 +0200
Subject: [PATCH] sumatools: drop

All derivations fail to build with GCC 14 and their repositories were
archived upstream [1]-[3].

[1] https://git.metabarcoding.org/obitools/sumaclust
[2] https://git.metabarcoding.org/obitools/sumalibs
[3] https://git.metabarcoding.org/obitools/sumatra
---
 .../science/biology/sumatools/default.nix     | 77 -------------------
 pkgs/top-level/aliases.nix                    |  3 +
 pkgs/top-level/all-packages.nix               |  6 --
 3 files changed, 3 insertions(+), 83 deletions(-)
 delete mode 100644 pkgs/applications/science/biology/sumatools/default.nix

diff --git a/pkgs/applications/science/biology/sumatools/default.nix b/pkgs/applications/science/biology/sumatools/default.nix
deleted file mode 100644
index fc07cd661c56..000000000000
--- a/pkgs/applications/science/biology/sumatools/default.nix
+++ /dev/null
@@ -1,77 +0,0 @@
-{
-  lib,
-  gccStdenv,
-  fetchFromGitLab,
-  zlib,
-}:
-
-let
-  stdenv = gccStdenv;
-  meta = with lib; {
-    description = "Fast and exact comparison and clustering of sequences";
-    homepage = "https://metabarcoding.org/sumatra";
-    maintainers = [ maintainers.bzizou ];
-    platforms = platforms.unix;
-  };
-
-in
-rec {
-
-  # Suma library
-  sumalibs = stdenv.mkDerivation rec {
-    version = "1.0.34";
-    pname = "sumalibs";
-    src = fetchFromGitLab {
-      domain = "git.metabarcoding.org";
-      owner = "obitools";
-      repo = pname;
-      rev = "sumalib_v${version}";
-      sha256 = "0hwkrxzfz7m5wdjvmrhkjg8kis378iaqr5n4nhdhkwwhn8x1jn5a";
-    };
-    makeFlags = [ "PREFIX=$(out)" ];
-    inherit meta;
-  };
-
-  # Sumatra
-  sumatra = stdenv.mkDerivation rec {
-    version = "1.0.34";
-    pname = "sumatra";
-    src = fetchFromGitLab {
-      domain = "git.metabarcoding.org";
-      owner = "obitools";
-      repo = pname;
-      rev = "${pname}_v${version}";
-      sha256 = "1bbpbdkshdc3xffqnr1qfy8qk64ldsmdc3s8mrcrlx132rgbi5f6";
-    };
-    buildInputs = [
-      sumalibs
-      zlib
-    ];
-    makeFlags = [
-      "LIBSUMA=${sumalibs}/lib/libsuma.a"
-      "LIBSUMAPATH=-L${sumalibs}"
-      "PREFIX=$(out)"
-    ];
-    inherit meta;
-  };
-
-  # Sumaclust
-  sumaclust = stdenv.mkDerivation rec {
-    version = "1.0.34";
-    pname = "sumaclust";
-    src = fetchFromGitLab {
-      domain = "git.metabarcoding.org";
-      owner = "obitools";
-      repo = pname;
-      rev = "${pname}_v${version}";
-      sha256 = "0x8yi3k3jxhmv2krp4rcjlj2f9zg0qrk7gx4kpclf9c3yxgsgrds";
-    };
-    buildInputs = [ sumalibs ];
-    makeFlags = [
-      "LIBSUMA=${sumalibs}/lib/libsuma.a"
-      "LIBSUMAPATH=-L${sumalibs}"
-      "PREFIX=$(out)"
-    ];
-    inherit meta;
-  };
-}
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index 3f0235e09a09..783637970235 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -1847,6 +1847,9 @@ mapAliases {
   suidChroot = throw "'suidChroot' has been dropped as it was unmaintained, failed to build and had questionable security considerations"; # Added 2025-05-17
   suitesparse_4_2 = throw "'suitesparse_4_2' has been removed as it was unmaintained upstream"; # Added 2025-05-17
   suitesparse_4_4 = throw "'suitesparse_4_4' has been removed as it was unmaintained upstream"; # Added 2025-05-17
+  sumaclust = throw "'sumaclust' has been removed as it was archived upstream and broken with GCC 14"; # Added 2025-06-14
+  sumalibs = throw "'sumalibs' has been removed as it was archived upstream and broken with GCC 14"; # Added 2025-06-14
+  sumatra = throw "'sumatra' has been removed as it was archived upstream and broken with GCC 14"; # Added 2025-06-14
   sumneko-lua-language-server = lua-language-server; # Added 2023-02-07
   sumokoin = throw "sumokoin has been removed as it was abandoned upstream"; # Added 2024-11-23
   supertag = throw "supertag has been removed as it was abandoned upstream and fails to build"; # Added 2025-04-20
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index a7e155283026..7ad31ce75ac1 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -15539,12 +15539,6 @@ with pkgs;
 
   samtools = callPackage ../applications/science/biology/samtools { };
 
-  inherit (callPackages ../applications/science/biology/sumatools { })
-    sumalibs
-    sumaclust
-    sumatra
-    ;
-
   trimmomatic = callPackage ../applications/science/biology/trimmomatic {
     jdk = pkgs.jdk21_headless;
     # Reduce closure size