insert exercise 4

8 files changed, 255 insertions, 0 deletions

diff --git a/day2/ex4-scanpy/default.nix b/day2/ex4-scanpy/default.nix
new file mode 100644
index 0000000..4d950cf
--- /dev/null
+++ b/day2/ex4-scanpy/default.nix
@@ -0,0 +1,72 @@
+/*
+This exercise is similar to the previous one, only in python instead of
+R for those who are more familar with python. For this example, we will
+make the scanpy tutorial notebook[1] reproducible.
+
+Unlike the R ecosysytem, Python dependency management is significantly
+more difficult. There is some tooling available for building
+reproducible Python environments, most notably mach-nix[2]. We will use
+this to provide an environment containing jupyter (for running the
+notebook) and scanpy; unfortunately scanpy has some unresolved bugs[2]
+and we will avoid them by pinning the anndata dependency to a known
+working version.
+
+This expression sets up the build directory to match the layout assumed
+by the notebook. Note that it also explicitly sets a Numba cache
+directory to the build directory: during a build the only writable
+location are the output paths allocated in the nix store and the
+(temporary) build directory.  Jupyter is executed to convert the
+notebook into a html file, and the output is copied to the store along
+with some ancillary h5 blobs produced by the notebook.
+
+Goal: As in exercise 3, the data cannot be fetched during execution as
+internet access is not permitted. Furthermore, the notebook itself also
+has to be retrieved. Fill out the required hashes for fetching these two
+pieces of data. Run the build, and review the output in a browser (e.g.,
+with `chromium ./result`).
+
+1: https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html
+2: https://github.com/DavHau/mach-nix
+*/
+{
+  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;
+  }
diff --git a/day2/ex4-scanpy/flake.lock b/day2/ex4-scanpy/flake.lock
new file mode 100755
index 0000000..eb5a579
--- /dev/null
+++ b/day2/ex4-scanpy/flake.lock
@@ -0,0 +1,103 @@
+{
+  "nodes": {
+    "bionix": {
+      "locked": {
+        "lastModified": 1664157112,
+        "narHash": "sha256-llJ4nRFxMhpy+tEywH1qzwcQjIQu5DCs6z2sIgel31w=",
+        "owner": "papenfusslab",
+        "repo": "bionix",
+        "rev": "81cfa50e6b345942951b68eac0e184ea025f2ae4",
+        "type": "github"
+      },
+      "original": {
+        "owner": "papenfusslab",
+        "repo": "bionix",
+        "type": "github"
+      }
+    },
+    "flake-utils": {
+      "locked": {
+        "lastModified": 1659877975,
+        "narHash": "sha256-zllb8aq3YO3h8B/U0/J1WBgAL8EX5yWf5pMj3G0NAmc=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "c0e246b9b83f637f4681389ecabcb2681b4f3af0",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "mach-nix": {
+      "inputs": {
+        "flake-utils": [
+          "flake-utils"
+        ],
+        "nixpkgs": [
+          "nixpkgs"
+        ],
+        "pypi-deps-db": [
+          "pypi-deps-db"
+        ]
+      },
+      "locked": {
+        "lastModified": 1654084003,
+        "narHash": "sha256-j/XrVVistvM+Ua+0tNFvO5z83isL+LBgmBi9XppxuKA=",
+        "owner": "DavHau",
+        "repo": "mach-nix",
+        "rev": "7e14360bde07dcae32e5e24f366c83272f52923f",
+        "type": "github"
+      },
+      "original": {
+        "id": "mach-nix",
+        "ref": "3.5.0",
+        "type": "indirect"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1659446231,
+        "narHash": "sha256-hekabNdTdgR/iLsgce5TGWmfIDZ86qjPhxDg/8TlzhE=",
+        "owner": "nixos",
+        "repo": "nixpkgs",
+        "rev": "eabc38219184cc3e04a974fe31857d8e0eac098d",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nixos",
+        "ref": "release-21.11",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "pypi-deps-db": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1665346953,
+        "narHash": "sha256-zU5SVQhz+t9W4pMm8LsN7tBTFMF9cOcO7kfzmoIPmRo=",
+        "owner": "DavHau",
+        "repo": "pypi-deps-db",
+        "rev": "6cb0a565a31ae61a61aff6f71dbdf2ee5bba8076",
+        "type": "github"
+      },
+      "original": {
+        "owner": "DavHau",
+        "repo": "pypi-deps-db",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "bionix": "bionix",
+        "flake-utils": "flake-utils",
+        "mach-nix": "mach-nix",
+        "nixpkgs": "nixpkgs",
+        "pypi-deps-db": "pypi-deps-db"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/day2/ex4-scanpy/flake.nix b/day2/ex4-scanpy/flake.nix
new file mode 100755
index 0000000..9587213
--- /dev/null
+++ b/day2/ex4-scanpy/flake.nix
@@ -0,0 +1,38 @@
+{
+  inputs = {
+    nixpkgs.url = "github:nixos/nixpkgs/release-21.11";
+    bionix.url = "github:papenfusslab/bionix";
+    flake-utils.url = "github:numtide/flake-utils";
+
+    mach-nix = {
+      url = "mach-nix/3.5.0";
+      inputs = {
+        nixpkgs.follows = "nixpkgs";
+        flake-utils.follows = "flake-utils";
+        pypi-deps-db.follows = "pypi-deps-db";
+      };
+    };
+
+    pypi-deps-db = {
+      url = "github:DavHau/pypi-deps-db";
+      flake = false;
+    };
+  };
+
+  outputs = {
+    self,
+    nixpkgs,
+    bionix,
+    flake-utils,
+    mach-nix,
+    ...
+  }:
+    flake-utils.lib.eachDefaultSystem (system: let
+      pkgs = import nixpkgs {
+        inherit system;
+      };
+      bionix' = import bionix {nixpkgs = pkgs;};
+    in {
+      defaultPackage = bionix'.callBionix ./. {mach-nix = mach-nix.lib."${system}";};
+    });
+}
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
@@ -0,0 +1,42 @@
+{
+  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;
+  }
diff --git a/day2/ex4-bwa/default.nix b/day2/ex5-bwa/default.nix
index 9c8356a..9c8356a 100644
--- a/day2/ex4-bwa/default.nix
+++ b/day2/ex5-bwa/default.nix
diff --git a/day2/ex4-bwa/flake.lock b/day2/ex5-bwa/flake.lock
index 981422e..981422e 120000
--- a/day2/ex4-bwa/flake.lock
+++ b/day2/ex5-bwa/flake.lock
diff --git a/day2/ex4-bwa/flake.nix b/day2/ex5-bwa/flake.nix
index bfaca96..bfaca96 100755
--- a/day2/ex4-bwa/flake.nix
+++ b/day2/ex5-bwa/flake.nix
diff --git a/day2/ex4-bwa/solution.nix b/day2/ex5-bwa/solution.nix
index 79fc7dc..79fc7dc 100644
--- a/day2/ex4-bwa/solution.nix
+++ b/day2/ex5-bwa/solution.nix