README.md

Week 1 - Begin working using JupyterHub, GitHub and git

1. Introduction
2. Learning Objectives with git and vim
3. Review Material
4. Lecture Material
5. Assignment
6. Project

Introduction

This week we will continue to learn how to work together in the OMICS course using GitHub and git on the command line in a JupyterHub terminal window.

Millions of people from all over the world build projects together using GitHub. There are thousands of biochemical projects availble for free as open-source projects in areas such as genomics, biochemistry, sequencing, and gene ontology enrichment available on GitHub. Major corporations have integrated open-source software into their workflows and products.

You won't want to miss the amazing projects that you can download and use. This class will begin to show how to interact with these amazing projects.

Learning Objectives

git

• Get experience with the daily flow of git:
  • git status
  • git add
  • git commit FILENAME.md -m 'Why I am commiting'
  • git commit -a -m 'Why I am commiting'
• Get experience with backing up your work to origin
  • git push
• Do your first pull request (PR)

vim

• Understand what a README.md conveys:
  • Welcome
  • We have been expecting you
  • Let me show you around
• Know how to navigate vim basics

Reading Material

• vim cheat sheet
• Why, of WHY, do those #?@! nutheads use vi?
• vim documentation on-line
• Why and How to use vim as a text editor
• vim keypresses on stackoverflow

Review Material

• The Arctic Code Vault

Project

Set up your OMICS project directory using git and GitHub.

In week 1's assignment you will create your own project directory (OMICS/projects/yourgitname) in this OMICS repo and initialize it with a README.md.

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