From 829d529c7caf3d6a3bd853e570de6bb71c7547a7 Mon Sep 17 00:00:00 2001
From: Alexis Praga <alexis.praga@proton.me>
Date: Sun, 6 Aug 2023 09:26:20 +0200
Subject: spip: unstable 2023-04-19

A genomic tool to compute splice preductions.
---
 pkgs/by-name/sp/spip/package.nix | 67 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 pkgs/by-name/sp/spip/package.nix

diff --git a/pkgs/by-name/sp/spip/package.nix b/pkgs/by-name/sp/spip/package.nix
new file mode 100644
index 0000000000000..9f99a9e438e09
--- /dev/null
+++ b/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";
+  };
+}
-- 
cgit 1.4.1