somatic-sniper: drop (#451893)

pkgs/by-name/so/somatic-sniper/package.nix

@@ -1,40 +0,0 @@
-{
-  lib,
-  stdenv,
-  fetchFromGitHub,
-  cmake,
-  zlib,
-  ncurses,
-}:
-
-stdenv.mkDerivation rec {
-  pname = "somatic-sniper";
-  version = "1.0.5.0";
-
-  src = fetchFromGitHub {
-    owner = "genome";
-    repo = "somatic-sniper";
-    rev = "v${version}";
-    sha256 = "0lk7p9sp6mp50f6w1nppqhr40fcwy1asw06ivw8w8jvvnwaqf987";
-  };
-
-  patches = [ ./somatic-sniper.patch ];
-
-  nativeBuildInputs = [ cmake ];
-  buildInputs = [
-    zlib
-    ncurses
-  ];
-
-  enableParallelBuilding = false;
-
-  meta = with lib; {
-    description = "Identify single nucleotide positions that are different between tumor and normal";
-    mainProgram = "bam-somaticsniper";
-    license = licenses.mit;
-    homepage = "https://github.com/genome/somatic-sniper";
-    maintainers = with maintainers; [ jbedo ];
-    platforms = platforms.linux;
-  };
-
-}

pkgs/by-name/so/somatic-sniper/somatic-sniper.patch

@@ -1,26 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 6d5a180..7254292 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -11,7 +11,7 @@ set(CMAKE_MODULE_PATH
-     )
- 
- include(TestHelper)
--include(VersionHelper)
-+#include(VersionHelper)
- include(ProjectHelper)
- 
- # NOTE: for sniper we want the exe suffix to be like 0.7.4, not just 0.7
-diff --git a/vendor/samtools.patch b/vendor/samtools.patch
-index f173017..654f878 100644
---- a/vendor/samtools.patch
-+++ b/vendor/samtools.patch
-@@ -6,7 +6,7 @@ diff -Nuar a/Makefile b/Makefile
-  
-  samtools:lib $(AOBJS)
- -		$(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -lz -L. -lbam
--+		$(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -L. -lbam -lz
-++		$(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lncurses -L. -lbam -lz
-  
-  razip:razip.o razf.o
-  		$(CC) $(CFLAGS) -o $@ razf.o razip.o -lz

pkgs/top-level/aliases.nix

@@ -2423,6 +2423,7 @@ mapAliases {
   snort2 = throw "snort2 has been removed as it is deprecated and unmaintained by upstream. Consider using snort (snort3) package instead."; # 2025-05-21
   snowman = throw "snowman has been removed as it is unmaintained by upstream"; # 2025-10-12
   soldat-unstable = opensoldat; # Added 2022-07-02
+  somatic-sniper = throw "somatic-sniper has been removed as it was archived in 2020 and fails to build."; # Added 2025-10-14
   soulseekqt = throw "'soulseekqt' has been removed due to lack of maintenance in Nixpkgs in a long time. Consider using 'nicotine-plus' or 'slskd' instead."; # Added 2025-06-07
   soundkonverter = throw "'soundkonverter' has been dropped as it depends on KDE Gear 5, and is unmaintained"; # Added 2025-08-20
   soundOfSorting = sound-of-sorting; # Added 2023-07-07