datascience-notebook-millefy

What's this?

datascience-notebook-millefy is a Docker image for running Millefy on JupyterLab. Millefy provides genome browser-like visualization of single-cell RNA sequensing (scRNA-seq) datasets.

DockerHub: https://hub.docker.com/r/yuifu/datascience-notebook-millefy/

How is it built?

Millefy (version 0.1.9 was) was installed in the Docker image of Jupyter Notebook Data Science Stack (jupyter/datascience-notebook:c88678a1c7c9; latest on 2018/03/30).

How to install

Build

cd Dockerfile
docker build -t yuifu/datascience-notebook-millefy:7a0c7325e470-v0.1.9 .

Pull

docker pull yuifu/datascience-notebook-millefy:7a0c7325e470-v0.1.9

How to use

Run by docker run

docker run -d --rm -p 4649:8888 \
-v "$PWD":/home/jovyan/work \
-e JUPYTER_ENABLE_LAB=1 \
--user root -e NB_UID=10011 -e GRANT_SUDO=yes \
yuifu/datascience-notebook-millefy:7a0c7325e470-v0.1.9 \
start-notebook.sh --NotebookApp.token=''

Run by docker-compose

Write docker-compose.yml as follows:

version: '2'
services:
  jupyter:
    image: yuifu/datascience-notebook-millefy:7a0c7325e470-v0.1.9
    environment:
      JUPYTER_ENABLE_LAB: 1
      NB_UID: 10011
      GRANT_SUDO: "yes"
    user: root
    ports:
      - 4649:8888
    volumes:
      - ./:/home/jovyan/work
      - ../test_data:/home/jovyan/test_data
    command: start-notebook.sh --NotebookApp.token=''

Then

docker-compose up -d

Use

After running a container, access localhost:4649 by your web browser.

For more information on Millefy itself, please refer to Millefy

Examples

test_millefy.ipynb

License

Copyright (c) 2018 Haruka Ozaki Released under the MIT license