jupyterNotebook.md

TL;DR

Jupyter notebook and jupyter lab are python notebook environments. Note that CTDS maintains several jupyter Docker images in https://github.com/uc-cdis/containers/

Jupyter Noteboboks

When running Jupyter Notebook workspaces we recommend using

"args": ["--NotebookApp.base_url=/lw-workspace/proxy/","--NotebookApp.password=''","--NotebookApp.token=''"],
"command": ["start-notebook.sh"],
"path-rewrite": "/lw-workspace/proxy/",
"ready-probe": "/lw-workspace/proxy/",
"user-uid": 1000,
"fs-gid": 100

to disable authentication as this is a single user container when run with Hatchery. This also sets the paths to be correct as well as the user IDs.

Jupyter Lab

Jupyter lab is the successor to jupyter notebook.

Example

{
      "target-port": 8888,
      "cpu-limit": "1.0",
      "memory-limit": "1024Mi",
      "name": "Jupyter Notebook Bio Python- Make your own",
      "image": "quay.io/occ_data/jupyternotebook:fix_niaid-test",
      "env": {"FRAME_ANCESTORS": "https://aids.niaiddata.org https://tb.niaiddata.org https://microbiome.niaiddata.org https://flu.niaiddata.org"},
      "args": ["--NotebookApp.base_url=/lw-workspace/proxy/","--NotebookApp.password=''","--NotebookApp.token=''"],
      "command": ["start-notebook.sh"],
      "path-rewrite": "/lw-workspace/proxy/",
      "use-tls": "false",
      "ready-probe": "/lw-workspace/proxy/",
      "lifecycle-post-start": ["/bin/sh","-c","export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; ln -s $(pwd) /home/$IAM/pd/dockerHome; mkdir -p /home/$IAM/.jupyter/custom; echo \"define(['base/js/namespace'], function(Jupyter){Jupyter._target = '_self';})\" >/home/$IAM/.jupyter/custom/custom.js; ln -s /data /home/$IAM/pd/; true"],
      "user-uid": 1000,
      "fs-gid": 100,
      "user-volume-location": "/home/jovyan/pd",
      "gen3-volume-location": "/home/jovyan/.gen3"
    },