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sumatools: drop

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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
This commit is contained in:
Tom Hunze 2025-06-14 11:28:47 +02:00
parent 9d2765dcee
commit 6f20f07dd7
No known key found for this signature in database
3 changed files with 3 additions and 83 deletions
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77
pkgs/applications/science/biology/sumatools/default.nix
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@ -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;
};
}

3
pkgs/top-level/aliases.nix
View File

@ -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 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_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 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 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 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 supertag = throw "supertag has been removed as it was abandoned upstream and fails to build"; # Added 2025-04-20

6
pkgs/top-level/all-packages.nix
View File

@ -15539,12 +15539,6 @@ with pkgs;
samtools = callPackage ../applications/science/biology/samtools { }; samtools = callPackage ../applications/science/biology/samtools { };
inherit (callPackages ../applications/science/biology/sumatools { })
sumalibs
sumaclust
sumatra
;
trimmomatic = callPackage ../applications/science/biology/trimmomatic { trimmomatic = callPackage ../applications/science/biology/trimmomatic {
jdk = pkgs.jdk21_headless; jdk = pkgs.jdk21_headless;
# Reduce closure size # Reduce closure size