From 10efa87252f948c3a0c75ff79637a9fa1946d201 Mon Sep 17 00:00:00 2001
From: patka <patka@patka.dev>
Date: Sat, 10 May 2025 19:08:13 +0200
Subject: [PATCH] samtools_0_1_19: drop

This version is from 2013 and not in anywhere within nixpkgs. We also have a 'samtools' that is up-to-date
---
 .../samtools/samtools-0.1.19-no-curses.patch  | 22 -----------
 .../biology/samtools/samtools_0_1_19.nix      | 39 -------------------
 pkgs/top-level/aliases.nix                    |  1 +
 pkgs/top-level/all-packages.nix               |  3 --
 4 files changed, 1 insertion(+), 64 deletions(-)
 delete mode 100644 pkgs/applications/science/biology/samtools/samtools-0.1.19-no-curses.patch
 delete mode 100644 pkgs/applications/science/biology/samtools/samtools_0_1_19.nix

diff --git a/pkgs/applications/science/biology/samtools/samtools-0.1.19-no-curses.patch b/pkgs/applications/science/biology/samtools/samtools-0.1.19-no-curses.patch
deleted file mode 100644
index a7782a1a0264..000000000000
--- a/pkgs/applications/science/biology/samtools/samtools-0.1.19-no-curses.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff --git a/Makefile b/Makefile
-index 2f51bfc..395d6f1 100644
---- a/Makefile
-+++ b/Makefile
-@@ -1,7 +1,7 @@
- CC=			gcc
- CFLAGS=		-g -Wall -O2
- #LDFLAGS=		-Wl,-rpath,\$$ORIGIN/../lib
--DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
-+DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE # -D_CURSES_LIB=1
- KNETFILE_O=	knetfile.o
- LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
- 			bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
-@@ -15,7 +15,7 @@ PROG=		samtools
- INCLUDES=	-I.
- SUBDIRS=	. bcftools misc
- LIBPATH=
--LIBCURSES=	-lcurses # -lXCurses
-+LIBCURSES=	# -lcurses # -lXCurses
- 
- .SUFFIXES:.c .o
- .PHONY: all lib
diff --git a/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix b/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix
deleted file mode 100644
index dddf33a536b3..000000000000
--- a/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix
+++ /dev/null
@@ -1,39 +0,0 @@
-{
-  lib,
-  stdenv,
-  fetchurl,
-  zlib,
-}:
-
-stdenv.mkDerivation rec {
-  pname = "samtools";
-  version = "0.1.19";
-
-  src = fetchurl {
-    url = "mirror://sourceforge/samtools/${pname}-${version}.tar.bz2";
-    sha256 = "d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4";
-  };
-
-  patches = [
-    ./samtools-0.1.19-no-curses.patch
-  ];
-
-  buildInputs = [ zlib ];
-
-  installPhase = ''
-    mkdir -p $out/bin
-    mkdir -p $out/share/man
-
-    cp samtools $out/bin
-    cp samtools.1 $out/share/man
-  '';
-
-  meta = with lib; {
-    description = "Tools for manipulating SAM/BAM/CRAM format";
-    mainProgram = "samtools";
-    license = licenses.mit;
-    homepage = "https://samtools.sourceforge.net/";
-    platforms = platforms.unix;
-    maintainers = [ maintainers.unode ];
-  };
-}
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index 08350e4c731c..e7f0acc74fdc 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -1644,6 +1644,7 @@ mapAliases {
   s2n = throw "'s2n' has been renamed to/replaced by 's2n-tls'"; # Converted to throw 2024-10-17
   sandboxfs = throw "'sandboxfs' has been removed due to being unmaintained, consider using linux namespaces for sandboxing instead"; # Added 2024-06-06
   sane-backends-git = throw "'sane-backends-git' has been renamed to/replaced by 'sane-backends'"; # Converted to throw 2024-10-17
+  samtools_0_1_19 = throw "'samtools_0_1_19' has been removed because it is unmaintained. Consider using 'samtools' instead"; # Added 2025-05-10
   scantailor = scantailor-advanced; # Added 2022-05-26
   schildichat-web = throw ''
     schildichat has been removed as it is severely lacking behind the Element upstream and does not receive regular security fixes.
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index b36a8a52b50d..7b5f1740ec25 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -15677,9 +15677,6 @@ with pkgs;
   raxml-mpi = raxml.override { useMpi = true; };
 
   samtools = callPackage ../applications/science/biology/samtools { };
-  samtools_0_1_19 = callPackage ../applications/science/biology/samtools/samtools_0_1_19.nix {
-    stdenv = gccStdenv;
-  };
 
   inherit (callPackages ../applications/science/biology/sumatools { })
     sumalibs