Workshop Details

Managing software versions, packages, and dependencies on Quest can be challenging. These challenges are multiplied when working with collaborators or sharing your workflow with others who want to reproduce it. Learn how to use environments, containers, and workflow management systems to ensure your research produces consistent results over timeThese challenges are multiplied when working with collaborators or trying to share your workflow with others who want to reproduce it. Learn how to use environments, containers, and workflow management systems to ensure your research produces consistent results overtime and can be reproduced by others.

Prerequisites: This workshop is designed for those who have attended Part 1 of Research Computing Basics and Beyond, or who already know how to transfer data to and from Quest, navigate Quest from the command line, and submit batch jobs.

Attendees will learn how to:

Create a virtual environment to manage software packages and versions

Set up a virtual environment optimized to use Quest’s GPU resources

Use and deploy Docker/Singularity containers to ensure a consistent computing environment across people and even different computing systems

Use GitHub to support setting up and managing containers

Use Nextflow to manage multipart computational workflows, including popular bioinformatic pipelines from nf-core

Develop a reproducible workflow that will support both you and others in achieving consistent results

Part 3: Software Environments, Containers, and Reproducibility