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

   1 {
   2  fetchFromGitHub,
   3  fetchurl,
   4  lib,
   5  makeWrapper,
   6  rPackages,
   7  rWrapper,
   8  stdenv
   9 }:
  10
  11 let
  12   my-r-packages = rWrapper.override{packages = with rPackages; [
  13     foreach
  14     doParallel
  15     randomForest
  16   ];};
  17   transcriptome-url = "https://kumisystems.dl.sourceforge.net/project/splicing-prediction-pipeline/transcriptome/";
  18
  19   transcriptome19 = fetchurl {
  20     url = transcriptome-url + "/transcriptome_hg19.RData";
  21     sha256 = "sha256-E8UmHoNoySSIde+TRE6bxVP0PrccpKDvIHBGCvWnYOw=";
  22   };
  23
  24   transcriptome38 = fetchurl {
  25     url = transcriptome-url + "/transcriptome_hg38.RData";
  26     sha256 = "sha256-mQMMZVN1byXMYjFoRdezmoZtnhUur2CHOP/j/pmw8as=";
  27   };
  28
  29 in
  30
  31 stdenv.mkDerivation {
  32   pname = "spip";
  33   version = "unstable-2023-04-19";
  34
  35   src = fetchFromGitHub {
  36     owner = "raphaelleman";
  37     repo = "SPiP";
  38     rev = "cae95fe0ee7a2602630b7a4eacbf7cfa0e1763f0";
  39     sha256 = "sha256-/CufUaQYnsdo8Rij/24JmixPgMi7o1CApLxeTneWAVc=";
  40   };
  41
  42   nativeBuildInputs = [ makeWrapper ];
  43   buildInput = [ my-r-packages ];
  44
  45   installPhase =''
  46     runHook preInstall
  47
  48     mkdir -p $out/bin
  49     cp SPiPv2.1_main.r $out/
  50     cp -r RefFiles $out/
  51     ln -s ${transcriptome19} $out/RefFiles/transcriptome_hg19.RData
  52     ln -s ${transcriptome38} $out/RefFiles/transcriptome_hg38.RData
  53     makeWrapper ${my-r-packages}/bin/Rscript $out/bin/spip \
  54       --add-flags "$out/SPiPv2.1_main.r"
  55
  56     runHook postInstall
  57 '';
  58
  59   meta = with lib; {
  60     description = "A random forest model for splice prediction in genomics";
  61     license     = licenses.mit;
  62     homepage    = "https://github.com/raphaelleman/SPiP";
  63     maintainers = with maintainers; [ apraga ];
  64     platforms = platforms.unix;
  65     mainProgram = "spip";
  66   };
  67 }