scanpy-nix-flake

Nix flake packaging scanpy and jupyter notebook server.

Usage

1. Install nix (if not yet installed)
2. Enable nix flakes (if not already)

   mkdir -p ~/.config/nix
   echo -e "experimental-features = nix-command flakes\n" >> ~/.config/nix/nix.conf

3. Install git (if you don't have it alerady installed)

   nix-env -i git

4. Build this flake and start the jupyter notebook server

   nix run github:ilya-kolpakov/scanpy-nix-flake -- --notebook-dir=/path/to/notebooks

   where /path/to/notebooks is the top-level directory to be served via the web UI. Add --ip=0.0.0.0 if you want to server to be accessible from other machines.

Docker image

Building:

nix build .#docker-image
# ./result points to a tar.gz image in nix store
readlink -e ./result
# /nix/store/<HASH>-docker-image-jupyter-scanpy.tar.gz

Using:

zcat jupyter-scanpy-<HASH>.tar.gz | sudo docker load
docker run -p 8888:8888 -v ../path/to/notebooks:/notebooks

Singularity image

First build the docker image, unzip the tar file and run

singularity build image.sif docker-archive://path/to/image.tar