From e63f2bec4611fbae5d4bfc0509652e98da4cd0c6 Mon Sep 17 00:00:00 2001
From: Guy Chronister <guychronister@outlook.com>
Date: Mon, 2 Feb 2026 16:32:23 -0600
Subject: [PATCH] cd-hit: migrate to by-name, move override

---
 .../cd-hit/default.nix => by-name/cd/cd-hit/package.nix}      | 4 ++--
 pkgs/top-level/all-packages.nix                               | 4 ----
 2 files changed, 2 insertions(+), 6 deletions(-)
 rename pkgs/{applications/science/biology/cd-hit/default.nix => by-name/cd/cd-hit/package.nix} (93%)

diff --git a/pkgs/applications/science/biology/cd-hit/default.nix b/pkgs/by-name/cd/cd-hit/package.nix
similarity index 93%
rename from pkgs/applications/science/biology/cd-hit/default.nix
rename to pkgs/by-name/cd/cd-hit/package.nix
index 0e3e4cd40750..11eb2fe7646f 100644
--- a/pkgs/applications/science/biology/cd-hit/default.nix
+++ b/pkgs/by-name/cd/cd-hit/package.nix
@@ -6,7 +6,7 @@
   zlib,
   perl,
   perlPackages,
-  openmp,
+  llvmPackages,
 }:
 
 stdenv.mkDerivation rec {
@@ -30,7 +30,7 @@ stdenv.mkDerivation rec {
     zlib
     makeWrapper
   ];
-  buildInputs = lib.optional stdenv.cc.isClang openmp;
+  buildInputs = lib.optional stdenv.cc.isClang llvmPackages.openmp;
 
   makeFlags = [
     "CC=${stdenv.cc.targetPrefix}c++" # remove once https://github.com/weizhongli/cdhit/pull/114 is merged
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index f9c943df90e8..3dc57d4b74a2 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -12158,10 +12158,6 @@ with pkgs;
 
   ### SCIENCE/BIOLOGY
 
-  cd-hit = callPackage ../applications/science/biology/cd-hit {
-    inherit (llvmPackages) openmp;
-  };
-
   deepdiff = with python3Packages; toPythonApplication deepdiff;
 
   deep-translator = with python3Packages; toPythonApplication deep-translator;