Included Software

The Breeder Genomics Hub uses the breeder-notebook as its base environment for all users. A nonexhaustive list of bundled software is included below.

The notebook environment and its associated software is a community endeavor, so if there’s something that you think should be included, please open an issue on the breeder-notebook GitHub repository.

Buckler Lab Software

Software developed by members of the Buckler Lab:

• TASSEL
• The Practical Haplotype Graph
• rTASSEL and rPHG

Innovation Lab for Crop Improvement

Software developed by members of the Feed the Future Innovation Lab for Crop Improvement:

• BrAPI Helper JupyterLab extension that provides GUI for managing database connections to breeding management systems (e.g. BMS, BreedBase, GIGWA)
• Notebook templates (using JupyterLab Templates) providing instruction on common bioinformatics and data science pipelines for breeders

Common Bioinformatics Tools

• minimap2
• samtools & bcftools
• bwa (Burrow-Wheeler Aligner)

Programming Languages

The JupyterLab environment comes with kernels for the following:

• Python
• R
• Kotlin

Installing Additional Software

If users wish to install packages via Apt, which requires super-user privileges, the Docker image used by the Hub will have to be modified. One can either open an issue on the breeder-notebook repository to request the package be added, fork the breeder-notebook, or substitute their own Docker image entirely.

The permanent storage can be configured to save the user’s entire home directory (everything in ~/) such that installed packages - e.g. via Conda - persist between server restarts. Although the breeder-notebook is designed to provide researchers the proverbial kitchen sink, it is understood that oftentimes specific dependencies are required in order to reproduce papers or make use of existing/legacy code. Simply adjust the DockerSpawner volumes like so:

c.DockerSpawner.volumes = { "breeder-{username}": "/home/jovyan" }

This will associate the user’s entire home directory with their volume on the host, allowing for all files to be persisted. Filesystem usage should be monitored, of course, to prevent accidental overuse of available disk space.

Specific configuration related to modifying package install locations (e.g. where R installs packages) is outside the scope of this documentation.