.gitpod.yml

image:
  file: .gitpod.Dockerfile

tasks:
  - name: Init Gitpod Workspace
    init: |
      pip3 install -r requirements.txt
      jupyter nbextension install --sys-prefix --py nbgrader
      jupyter nbextension enable --sys-prefix --py nbgrader
      jupyter labextension enable nbgrader
      #conda install --yes -c bioconda bwa blast samtools --solver=libmamba
      conda clean --all --yes
    command: |
      echo "Running: $GITPOD_WORKSPACE_URL"
      echo "Call 'gogo w' to work on workshop material in Jupyter lab."

ports:
  - name: Jupyter Notebook
    port: 8888
    onOpen: open-browser

vscode:
  extensions:
    - eamodio.gitlens
    - janisdd.vscode-edit-csv
    - mechatroner.rainbow-csv
    - ms-python.python
    - ms-python.debugpy