Unverified Commit 63b875e0 authored by Zitrone's avatar Zitrone Committed by GitHub
Browse files

SPAdes: refactor

parent 80f3f19e

pkgs/applications/science/biology/spades/default.nix

deleted100644 → 0
+0 −32
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{ lib, stdenv, fetchurl, zlib, bzip2, cmake, python3 }:



stdenv.mkDerivation rec {

  pname = "SPAdes";

  version = "3.15.5";



  src = fetchurl {

    url = "http://cab.spbu.ru/files/release${version}/${pname}-${version}.tar.gz";

    sha256 = "sha256-FVw2QNVx8uexmgUDHR/Q0ZvYLfeF04hw+5O9JBsSu/o=";

  };



  nativeBuildInputs = [ cmake ];



  buildInputs = [ zlib bzip2 python3 ];



  doCheck = true;



  sourceRoot = "${pname}-${version}/src";



  env.CXXFLAGS = toString [

    # GCC 13: error: 'uint32_t' does not name a type

    "-include cstdint"

  ];



  meta = with lib; {

    description = "St. Petersburg genome assembler: assembly toolkit containing various assembly pipelines";

    license = licenses.gpl2Only;

    homepage = "http://cab.spbu.ru/software/spades/";

    platforms = [ "x86_64-linux" "x86_64-darwin" ];

    maintainers = [ maintainers.bzizou ];

  };

}

pkgs/by-name/sp/spades/package.nix

0 → 100644
+46 −0
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{

  lib,

  stdenv,

  fetchurl,

  zlib,

  bzip2,

  cmake,

  python3,

}:



stdenv.mkDerivation (finalAttrs: {

  pname = "spades";

  version = "3.15.5";



  src = fetchurl {

    url = "https://github.com/ablab/spades/releases/download/v${finalAttrs.version}/SPAdes-${finalAttrs.version}.tar.gz";

    hash = "sha256-FVw2QNVx8uexmgUDHR/Q0ZvYLfeF04hw+5O9JBsSu/o=";

  };

  sourceRoot = "SPAdes-${finalAttrs.version}/src";



  env.CXXFLAGS = toString [

    # GCC 13: error: 'uint32_t' does not name a type

    "-include cstdint"

  ];



  nativeBuildInputs = [ cmake ];



  buildInputs = [

    zlib

    bzip2

    python3

  ];



  doCheck = true;



  meta = {

    description = "St. Petersburg genome assembler, a toolkit for assembling and analyzing sequencing data";

    license = lib.licenses.gpl2Only;

    homepage = "http://ablab.github.io/spades";

    platforms = [

      "x86_64-linux"

      "x86_64-darwin"

    ];

    maintainers = with lib.maintainers; [ bzizou ];

  };

})

pkgs/top-level/aliases.nix

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@@ -1228,6 +1228,7 @@ mapAliases ({ 
  solr = throw "'solr' has been removed from nixpkgs, as it was broken and unmaintained"; # Added 2023-03-16

  soundOfSorting = sound-of-sorting; # Added 2023-07-07

  soundux = throw "'soundux' has been removed, as it is unmaintained."; # Added on 2024-02-14

  SPAdes = spades; # Added 2024-06-12

  spark2 = throw "'spark2' is no longer supported nixpkgs, please use 'spark'"; # Added 2023-05-08

  spark_2_4 = throw "'spark_2_4' is no longer supported nixpkgs, please use 'spark'"; # Added 2023-05-08

  spark_3_1 = throw "'spark_3_1' is no longer supported nixpkgs, please use 'spark'"; # Added 2023-05-08

pkgs/top-level/all-packages.nix

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@@ -37945,8 +37945,6 @@ with pkgs; 














  seaview = callPackage ../applications/science/biology/seaview { };



























  SPAdes = callPackage ../applications/science/biology/spades { };



























  svaba = callPackage ../applications/science/biology/svaba { };





























  tandem-aligner = callPackage ../applications/science/biology/tandem-aligner { };