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 a4e9de4208c8..45a73a9b2a34 100644 --- a/pkgs/top-level/aliases.nix +++ b/pkgs/top-level/aliases.nix @@ -1856,6 +1856,9 @@ 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 94b5763734ed..79564bb1b3b5 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -15500,12 +15500,6 @@ 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