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+/*
+This example tries to demonstrate that even very simple workflows (this
+is only really one computational stage) can benefit from some formalisation
+to provide reproducibility. We borrow part of the edgeR example available from
+https://ucdavis-bioinformatics-training.github.io/2018-September-Bioinformatics-Prerequisites/friday/limma_biomart_vignettes.html
+and specify it in BioNix so that it's easily reproducible.
+
+One key learning goal in this exercise is to understand that Nix only
+allows _inputs_ to be referenced during the execution of a build to
+prevent side effects from creeping in. In particular, internet access is
+forbidden when the build sandbox is enabled (default, but not on Milton
+for technical reasons), meaning data cannot be fetched as part of a
+build as the original example does.
+
+We therefore fetch the count input as a separate stage and Nix will take
+care of downloading it for us. The caveate is that the content of things
+fetched from the internet must be verified to give reproducibility. Nix
+does this through hashing.
+
+Goal: fill out the below to specify required R packages, execute the
+build and observe the hash collision. Update the hash and see if the
+build now completes successfully.
+*/
+{bionix}:
+with bionix; let
+  R = pkgs.rWrapper.override {packages = with pkgs.rPackages; [];};
+
+  counts = pkgs.fetchurl {
+    url = "https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2018-September-Bioinformatics-Prerequisites/master/friday/counts.tsv";
+    sha256 = "sha256-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA=";
+  };
+in
+  stage {
+    inherit counts;
+    name = "r-ex";
+
+    buildInputs = [R];
+
+    buildCommand = ''
+      Rscript ${./script.R}
+    '';
+  }