spip: unstable 2023-04-19

A genomic tool to compute splice preductions.

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

@@ -0,0 +1,67 @@
+{
+ fetchFromGitHub,
+ fetchurl,
+ lib,
+ makeWrapper,
+ rPackages,
+ rWrapper,
+ stdenv
+}:
+
+let
+  my-r-packages = rWrapper.override{packages = with rPackages; [
+    foreach
+    doParallel
+    randomForest
+  ];};
+  transcriptome-url = "https://kumisystems.dl.sourceforge.net/project/splicing-prediction-pipeline/transcriptome/";
+
+  transcriptome19 = fetchurl {
+    url = transcriptome-url + "/transcriptome_hg19.RData";
+    sha256 = "sha256-E8UmHoNoySSIde+TRE6bxVP0PrccpKDvIHBGCvWnYOw=";
+  };
+
+  transcriptome38 = fetchurl {
+    url = transcriptome-url + "/transcriptome_hg38.RData";
+    sha256 = "sha256-mQMMZVN1byXMYjFoRdezmoZtnhUur2CHOP/j/pmw8as=";
+  };
+
+in
+
+stdenv.mkDerivation {
+  pname = "spip";
+  version = "unstable-2023-04-19";
+
+  src = fetchFromGitHub {
+    owner = "raphaelleman";
+    repo = "SPiP";
+    rev = "cae95fe0ee7a2602630b7a4eacbf7cfa0e1763f0";
+    sha256 = "sha256-/CufUaQYnsdo8Rij/24JmixPgMi7o1CApLxeTneWAVc=";
+  };
+
+  nativeBuildInputs = [ makeWrapper ];
+  buildInput = [ my-r-packages ];
+
+  installPhase =''
+    runHook preInstall
+
+    mkdir -p $out/bin
+    cp SPiPv2.1_main.r $out/
+    cp -r RefFiles $out/
+    ln -s ${transcriptome19} $out/RefFiles/transcriptome_hg19.RData
+    ln -s ${transcriptome38} $out/RefFiles/transcriptome_hg38.RData
+    makeWrapper ${my-r-packages}/bin/Rscript $out/bin/spip \
+      --add-flags "$out/SPiPv2.1_main.r"
+
+    runHook postInstall
+'';
+
+  meta = with lib; {
+    description = "A random forest model for splice prediction in genomics";
+    license     = licenses.mit;
+    homepage    = "https://github.com/raphaelleman/SPiP";
+    maintainers = with maintainers; [ apraga ];
+    platforms = platforms.unix;
+    mainProgram = "spip";
+  };
+}

pkgs/top-level/all-packages.nix

@@ -13379,6 +13379,8 @@ with pkgs;
 
   spicy = callPackage ../development/tools/spicy { };
 
+  spip = callPackage ../by-name/sp/spip/package.nix { };
+
   spire = callPackage ../tools/security/spire { };
   # to match naming of other package repositories
   spire-agent = spire.agent;