➔ Conda Slides, Container Slides
This workshop is aimed at people with some experience developing tools but may also be of use to deployers who need to manage complex sets of dependencies for tools.
Galaxy tools define the applications and other dependencies they require to run using their requirements section. This training session will cover the elements of the requirements section and how Galaxy can be configured to utilize these.
The current best practice for resolving these dependencies is using Conda and Bioconda, and so a substantial amount of time will be spent on these topics. We will go through the process of creating, testing, and publishing a Bioconda package. We will work through an example of connecting these packages to Galaxy.
We will also discuss how the Biocontainers project constructs Docker containers from Bioconda packages and how to emulate this process for local testing before publication. Finally, we will review approaches to leveraging these containers from Galaxy to run jobs within containers.
Prerequisites:
