1 files changed, 42 insertions, 0 deletions
diff --git a/day2/ex4-scanpy/solution.nix b/day2/ex4-scanpy/solution.nix
new file mode 100644
index 0000000..dcc2037
--- /dev/null
+++ b/day2/ex4-scanpy/solution.nix
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+{
+  bionix,
+  mach-nix,
+}:
+with bionix; let
+  python = mach-nix.mkPython {
+    requirements = ''
+      jupyterlab
+      scanpy
+      anndata=0.7.8
+      leidenalg
+    '';
+  };
+in
+  stage {
+    name = "scanpy-tutorial.html";
+    buildInputs = [python];
+    outputs = ["out" "results"];
+
+    src = pkgs.fetchurl {
+      url = "http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz";
+      sha256 = "sha256-hH1uvZoeyado8r5+QMpCy/516+ttdqTCQWcEFpncKLU=";
+    };
+
+    notebook = pkgs.fetchurl {
+      url = "https://github.com/scverse/scanpy-tutorials/raw/532f755ac31d9baf00116a44243b73174765a6a6/pbmc3k.ipynb";
+      sha256 = "sha256-mwIPHKAsDd1F4F9fNnAfrapBehBN3jjEsrLGsI37Igg=";
+    };
+
+    buildCommand = ''
+      export NUMBA_CACHE_DIR=$TMPDIR
+      cp $notebook notebook.ipynb
+      mkdir data
+      tar -zxf $src -C data
+      mkdir write
+      jupyter nbconvert  --execute --to html ./notebook.ipynb
+      cp notebook.html $out
+      cp -r write $results
+    '';
+
+    stripStorePaths = false;
+  }