Commit 2b379578 authored by Benjamin Sparks's avatar Benjamin Sparks Committed by Masum Reza
Browse files

manta: drop 

manta depends on Python 2.6+, and does not support Python 3.
Upstream archived development on Jul 17 2023.
parent 35495326

pkgs/by-name/ma/manta/package.nix

deleted100644 → 0
+0 −37
Original line number Diff line number Diff line 
{ lib, stdenv, fetchFromGitHub, cmake, zlib, python2 }:



stdenv.mkDerivation rec {

  pname = "manta";

  version = "1.6.0";



  src = fetchFromGitHub {

    owner = "Illumina";

    repo = "manta";

    rev = "v${version}";

    sha256 = "1711xkcw8rpw9xv3bbm7v1aryjz4r341rkq5255192dg38sgq7w2";

  };



  nativeBuildInputs = [ cmake ];

  buildInputs = [ zlib python2 ];

  postFixup = ''

    sed -i 's|/usr/bin/env python2|${python2.interpreter}|' $out/lib/python/makeRunScript.py

    sed -i 's|/usr/bin/env python|${python2.interpreter}|' $out/lib/python/pyflow/pyflow.py

    sed -i 's|/bin/bash|${stdenv.shell}|' $out/lib/python/pyflow/pyflowTaskWrapper.py

  '';

  doInstallCheck = true;

  installCheckPhase = ''

    rm $out/lib/python/**/*.pyc

    PYTHONPATH=$out/lib/python:$PYTHONPATH python -c 'import makeRunScript'

    PYTHONPATH=$out/lib/python/pyflow:$PYTHONPATH python -c 'import pyflowTaskWrapper; import pyflow'

  '';



  env.NIX_CFLAGS_COMPILE = "-Wno-error=array-bounds";



  meta = with lib; {

    description = "Structural variant caller";

    license = licenses.gpl3;

    homepage = "https://github.com/Illumina/manta";

    maintainers = with maintainers; [ jbedo ];

    platforms =  platforms.x86_64;

  };

}

pkgs/top-level/aliases.nix

+1 −0
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@@ -939,6 +939,7 @@ mapAliases { 
  mariadb-client = hiPrio mariadb.client; #added 2019.07.28

  maligned = throw "maligned was deprecated upstream in favor of x/tools/go/analysis/passes/fieldalignment"; # Added 20204-08-24

  manicode = throw "manicode has been renamed to codebuff"; # Added 2024-12-10

  manta = throw "manta does not support python3, and development has been abandoned upstream"; # Added 2025-03-17

  marwaita-manjaro = lib.warnOnInstantiate "marwaita-manjaro has been renamed to marwaita-teal" marwaita-teal; # Added 2024-07-08

  marwaita-peppermint = lib.warnOnInstantiate "marwaita-peppermint has been renamed to marwaita-red" marwaita-red; # Added 2024-07-01

  marwaita-ubuntu = lib.warnOnInstantiate "marwaita-ubuntu has been renamed to marwaita-orange" marwaita-orange; # Added 2024-07-08