From c54a339de47cc26b400ee8529a96d2cde70debb4 Mon Sep 17 00:00:00 2001
From: Benjamin Sparks <b.sparks@alugha.com>
Date: Mon, 17 Mar 2025 21:57:49 +0100
Subject: [PATCH] strelka: drop

strelka depends on Python 2.6+, and does not support Python 3.
---
 pkgs/by-name/st/strelka/package.nix | 76 -----------------------------
 pkgs/top-level/aliases.nix          |  1 +
 2 files changed, 1 insertion(+), 76 deletions(-)
 delete mode 100644 pkgs/by-name/st/strelka/package.nix

diff --git a/pkgs/by-name/st/strelka/package.nix b/pkgs/by-name/st/strelka/package.nix
deleted file mode 100644
index a7470394213c3..0000000000000
--- a/pkgs/by-name/st/strelka/package.nix
+++ /dev/null
@@ -1,76 +0,0 @@
-{
-  lib,
-  stdenv,
-  fetchFromGitHub,
-  fetchpatch,
-  cmake,
-  boost,
-  zlib,
-  python2,
-}:
-
-stdenv.mkDerivation rec {
-  pname = "strelka";
-  version = "2.9.10";
-
-  src = fetchFromGitHub {
-    owner = "Illumina";
-    repo = "strelka";
-    rev = "v${version}";
-    sha256 = "1nykbmim1124xh22nrhrsn8xgjb3s2y7akrdapn9sl1gdych4ppf";
-  };
-
-  patches = [
-    # Pull pending fix for gcc-12:
-    #   https://github.com/Illumina/strelka/pull/204
-    (fetchpatch {
-      name = "limits.patch";
-      url = "https://github.com/Illumina/strelka/commit/98272cd345c6e4c672e6a5b7721204fcac0502d6.patch";
-      hash = "sha256-psBiuN32nvwZ+QX51JQjIdRhEE3k7PfwbkD10ckqvZk=";
-    })
-  ];
-
-  postPatch = ''
-    substituteInPlace src/cmake/boost.cmake \
-      --replace "1.58.0" "${boost.version}" \
-      --replace "Boost_USE_STATIC_LIBS ON" "Boost_USE_STATIC_LIBS OFF"
-  '';
-
-  nativeBuildInputs = [ cmake ];
-  buildInputs = [
-    boost
-    zlib
-    python2
-  ];
-
-  cmakeFlags = [
-    "-DCMAKE_CXX_STANDARD=14"
-  ];
-
-  env.NIX_CFLAGS_COMPILE = toString [
-    "-Wno-error=maybe-uninitialized"
-    "-Wno-error=pessimizing-move"
-  ];
-
-  preConfigure = ''
-    sed -i 's|/usr/bin/env python|${python2}/bin/python|' src/python/lib/makeRunScript.py
-    patchShebangs .
-  '';
-
-  postFixup = ''
-    pushd $out/lib/python/pyflow
-    sed -i 's|/bin/bash|${stdenv.shell}|' pyflowTaskWrapper.py
-    rm pyflowTaskWrapper.pyc
-    echo "import pyflowTaskWrapper" | python2
-    popd
-  '';
-
-  meta = with lib; {
-    description = "Germline and small variant caller";
-    license = licenses.gpl3;
-    homepage = "https://github.com/Illumina/strelka";
-    maintainers = with maintainers; [ jbedo ];
-    platforms = platforms.linux;
-  };
-
-}
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index 06c976b74e57e..faee608994ca3 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -1460,6 +1460,7 @@ mapAliases {
   steam-run-native = steam-run; # added 2022-02-21
   StormLib = stormlib; # Added 2024-01-21
   strawberry-qt5 = throw "strawberry-qt5 has been replaced by strawberry-qt6"; # Added 2024-11-22
+  strelka = throw "strelka depends on Python 2.6+, and does not support Python 3."; # Added 2025-03-17
   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
   swiProlog = lib.warnOnInstantiate "swiProlog has been renamed to swi-prolog" swi-prolog; # Added 2024-09-07