Anopheles genomic surveillance

This repository holds lecture notes for a training course on genomic surveillance of Anopheles mosquitoes, which are vectors of malaria.

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

Maintainer notes

Checking the notebooks

Please see the video below for a guide to how to check the lecture notebooks for any problems and report any issues you find:

• https://youtu.be/DrVCqSrfAV8 -- guide to checking notebooks

Development environment setup

Here are instructions for getting set up to work on this project.

Fork this GitHub repository to your own GitHub account.

Clone your fork. E.g.:

git clone git@github.com:alimanfoo/anopheles-genomic-surveillance.github.io.git
cd anopheles-genomic-surveillance.github.io

Create a Python virtual environment to use as the development environment. There are various different ways to create a virtual environment. E.g., if you have virtualenvwrapper:

mkvirtualenv --python=/usr/bin/python3.7 anopheles-genomic-surveillance-dev

Then activate your development environment, e.g.:

workon anopheles-genomic-surveillance-dev

Then you can install requirements:

pip install -r requirements.txt

Building the book

The training course website is built using jupyterbook. From your local clone of the repo, first ensure you have activated your development environment, e.g.:

workon anopheles-genomic-surveillance-dev

...then you can build the book:

jb build docs

This should render the book as HTML files. The command will show where the HTML files have been created, so you can preview them in a browser.

In some cases you may need to preview the HTML files via an HTTP server. You can run an HTTP server locally with this command:

python -m http.server --directory docs/_build/html