From 492e5e07c9f2d622e776fcc2887ecded5edf0a43 Mon Sep 17 00:00:00 2001
From: Martin Weinelt <hexa@darmstadt.ccc.de>
Date: Wed, 12 Jan 2022 02:33:33 +0100
Subject: [PATCH] lumpy: drop

Removed because it requires python2 and the upstream repository looks
undermaintained.
---
 .../science/biology/lumpy/default.nix         | 50 -------------------
 pkgs/top-level/aliases.nix                    |  1 +
 pkgs/top-level/all-packages.nix               |  2 -
 3 files changed, 1 insertion(+), 52 deletions(-)
 delete mode 100644 pkgs/applications/science/biology/lumpy/default.nix

diff --git a/pkgs/applications/science/biology/lumpy/default.nix b/pkgs/applications/science/biology/lumpy/default.nix
deleted file mode 100644
index 91a001744474..000000000000
--- a/pkgs/applications/science/biology/lumpy/default.nix
+++ /dev/null
@@ -1,50 +0,0 @@
-{ lib, stdenv, fetchFromGitHub, htslib, zlib, curl, openssl, samblaster, sambamba
-, samtools, hexdump, python2Packages, which }:
-
-let
-  python =
-    python2Packages.python.withPackages (pkgs: with pkgs; [ pysam numpy ]);
-
-in stdenv.mkDerivation rec {
-  pname = "lumpy";
-  version = "0.3.1";
-
-  src = fetchFromGitHub {
-    owner = "arq5x";
-    repo = "lumpy-sv";
-    rev = "v${version}";
-    sha256 = "0r71sg7qch8r6p6dw995znrqdj6q49hjdylhzbib2qmv8nvglhs9";
-    fetchSubmodules = true;
-  };
-
-  nativeBuildInputs = [ which ];
-  buildInputs =
-    [ htslib zlib curl openssl python samblaster sambamba samtools hexdump ];
-
-  preConfigure = ''
-    patchShebangs ./.
-
-    # Use Nix htslib over bundled version
-    sed -i 's/lumpy_filter: htslib/lumpy_filter:/' Makefile
-    sed -i 's|../../lib/htslib/libhts.a|-lhts|' src/filter/Makefile
-    # Also make sure we use the includes from Nix's htslib
-    sed -i 's|../../lib/htslib/|${htslib}|' src/filter/Makefile
-  '';
-
-  # Upstream's makefile doesn't have an install target
-  installPhase = ''
-    mkdir -p $out
-    cp -r bin $out
-    cp -r scripts $out
-    sed -i 's|/build/source|'$out'|' $out/bin/lumpyexpress.config
-  '';
-
-  meta = with lib; {
-    description = "Probabilistic structural variant caller";
-    homepage = "https://github.com/arq5x/lumpy-sv";
-    maintainers = with maintainers; [ jbedo ];
-    license = licenses.mit;
-    platforms = [ "x86_64-linux" ];
-  };
-
-}
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index 9ba9da478834..acab25e64b48 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -568,6 +568,7 @@ mapAliases ({
   lua5_1_sockets = lua51Packages.luasocket; # added 2017-05-02
   lua5_expat = luaPackages.luaexpat; # added 2017-05-02
   lua5_sec = luaPackages.luasec; # added 2017-05-02
+  lumpy = throw "lumpy has been removed from nixpkgs, as it is stuck on python2."; # added 2022-01-12
   lxappearance-gtk3 = throw "lxappearance-gtk3 has been removed. Use lxappearance instead, which now defaults to Gtk3";  # added 2020-06-03
   lzma = xz; # moved from top-level 2021-03-14
   m3d-linux = m33-linux; # added 2016-08-13
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 276c490abf0b..8fd116aeeabd 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -31669,8 +31669,6 @@ with pkgs;
 
   last = callPackage ../applications/science/biology/last { };
 
-  lumpy = callPackage ../applications/science/biology/lumpy { };
-
   macse = callPackage ../applications/science/biology/macse { };
 
   MACS2 = callPackage ../applications/science/biology/MACS2 { };