README.md

notebooks

Jupyter notebook demo of sequgen functionality.

Prerequisites

For running locally on Ubuntu:

sudo apt install git

Running the notebooks locally

First clone this repository.

git clone https://github.com/sequgen/notebooks.git .

Install the dependencies with

# Create a virtualenv, e.g. with
python3 -m venv env

# activate virtualenv
source env/bin/activate

# make sure to have a recent version of pip
pip install --upgrade pip wheel

# (from the repository root directory)
# install sequgen + jupyter
pip install --requirement requirements.txt

# add the new local environment to jupyter
ipython kernel install --name sequgen-demo --user

Start the notebook server:

jupyter lab

It will open a web browser with the Jupyter Lab environment, in file-browser on left side bar open the notebook (*.ipynb files) of interest. Select the kernel sequgen-demo to run the notebook.