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Research Computing Starter Pack

Setup

Reproducibility Principles and Practices

Overview

1. Principles of Reproducibility
2. Primary Practices
3. Secondary Practices
4. Case-by-case Practices

Appendix: References

Introduction to the Command Line

Overview

1. Interacting with Computers
2. Browsing Files
3. Going Beyond Browsing
4. Editing Files

Appendix: References

Installing Software with Pixi

Overview

1. Environment Managers
2. Pixi Basics

Unit A: Configuring the Shell
Unit B: UC Davis HPC Modules
Unit C: Python Packages
Unit D: R Packages

Introduction to Version Control

Overview

1. Version Control Systems
2. Git Basics
3. Remote Repositories
4. The Git Workflow

Git for Teams

Overview

1. Branches & Merges
2. Working with GitHub
3. Making Git Comfortable

Building Workflows and Pipelines

Overview

1. Workflow Managers
2. Pixi Tasks
3. Snakemake

Unit A: The targets Package

Repository
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By Nick Ulle, Carl Stahmer, Tyler Shoemaker, and Wesley Brooks