Installing Jupyter Notebook environment

Jupyter environment using Conda

A Conda environment named: jupyter with Python 3.6+ should be created for running all Jupyter notebooks.

localhost:~> wget https://raw.githubusercontent.com/ncbi/cwl-ngs-workflows-cbb/master/requirements/conda-jupyter.yaml
localhost:~> conda env create -f conda-jupyter.yaml

Usage with Conda

For using the Conda environment

localhost:~> conda activate jupyter

Jupyter environment using Python virtual environment

Python 3.6+ should be installed. Then, a virtual environment should be created from the requirements file and these commands:

localhost:~> wget https://raw.githubusercontent.com/ncbi/pm4ngs/master/%7B%7Bcookiecutter.project_name%7D%7D/requirements/python.txt
localhost:~> virtualenv -p `which python3` venv
localhost:~> source venv/bin/activate
localhost:~> pip install -r python.txt

Usage with Python virtual environment

For using the Python virtual environment

localhost:~> source venv/bin/activate