From 059034ab3d5c40c8ef0350c440d4ae343802ec5c Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 10 Oct 2022 10:48:02 +1100
Subject: update ex2 to DE example

---
 day2/ex3-R/solution.nix | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

(limited to 'day2/ex3-R/solution.nix')

diff --git a/day2/ex3-R/solution.nix b/day2/ex3-R/solution.nix
index 7d40f88..406e1f3 100644
--- a/day2/ex3-R/solution.nix
+++ b/day2/ex3-R/solution.nix
@@ -1,19 +1,20 @@
 {bionix}:
 with bionix; let
-  R = pkgs.rWrapper.override {packages = with pkgs.rPackages; [edgeR];};
-
-  counts = pkgs.fetchurl {
-    url = "https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2018-September-Bioinformatics-Prerequisites/master/friday/counts.tsv";
-    sha256 = "sha256-ZmZ+vC4mKnmZKVJqbnEujDngwnSTZAxvQaZaNClUUWE=";
-  };
+  R = pkgs.rWrapper.override {packages = with pkgs.rPackages; [limma edgeR Mus_musculus RColorBrewer R_utils];};
 in
   stage {
-    inherit counts;
     name = "r-ex";
 
+    src = pkgs.fetchurl {
+      url = "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE63310&format=file";
+      sha256 = "sha256-jLII/e+SVNx4Fivb65WOF566fwFXFtdNLUs04S82++g=";
+    };
+
     buildInputs = [R];
 
     buildCommand = ''
+      tar xf $src
+      mkdir $out
       Rscript ${./script.R}
     '';
   }
-- 
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