Breeder Genomics Hub

🧬 Experimental / Alpha-Quality Software 🧪

The Breeder Genomics Hub is a batteries-included JupyterHub distribution for breeders (Pangeo for plant scientists).

Please refer to the documentation website for more information, in particular:

• Getting started with the Breeder Genomics Hub in your lab
• Example with notes on how the Buckler Lab uses the Breeder Genomics Hub alongside a RESTful PHG web server (see the example/ directory of this repo for configs)
• When to use the Breeder Genomics Hub, and alternatives like TLJH and Z2JH

The breeder-notebook Jupyter Docker Stack is the end-user environment, and contains common bioinformatics software useful to plant scientists and breeders, such as rPHG and rTASSEL. Before running the Breeder Genomics Hub, make sure to install this notebook image:

docker pull maizegenetics/breeder-notebook:latest

Development

Documentation

Documentation is hosted via GitHub Pages, which provides easy Jekyll integration.

To build the docs site locally:

cd docs
bundle install
bundle exec jekyll serve

Requires Ruby.

Note that in the docs there are places where lines of code are linked to on GitHub. If certain files are changed, it will require these links be updated. Use grep -r '#L' . to find them.