COMP90016-envs

Environment settings for workshops in Computational Genomics

Working with Gitpod

If working on this repo from a Gitpod workspace dependancies from the Dockerfile should be automatically installed and enabled in the base conda environment along with any packages listed in requirements.txt.

You will need to conda install any non-pip packages.

Opening a Jupyter session from Gitpod

# Increase gitpod timeout setting
gp timeout set 1h

# Launch jupyter-lab
jupyter lab --NotebookApp.allow_origin='*' --NotebookApp.allow_remote_access=True --NotebookApp.token='' --NotebookApp.password='' --no-browser --port=8888

# or use jupyter-notebook
jupyter notebook --NotebookApp.allow_origin='*' --NotebookApp.allow_remote_access=True --NotebookApp.token='' --NotebookApp.password='' --no-browser --port=8888

The notebook will be available on port 8888 by default. You can open this port using the link in the Ports tab above the terminal.

Note: See other gitpod settings here.

Binder

Open a Binder session using the environment settings from this repo.