Introduction to Git and GitHub
==

URL: https://hackmd.io/@k8hertweck/GitHub

**Sign in to each class meeting** [here](https://goo.gl/forms/j4MbWJuPoIYeJET12)

Have you installed GitHub Desktop and text editor? Have you signed up for a GitHub account? Instructions [here](https://github.com/fredhutchio/fredhutch.io/blob/gh-pages/software.md#git-and-github)

This page is for easy access to links we'll use during class. You don't need to do anything with this information until directed by your instructor.

If you have feedback about this course, please
[comment here](https://goo.gl/forms/Bw8dTV0Wghq2iG5i2)

Complete class notes [here](https://fredhutchio.github.io/git_github_intro/)

## Class 1: git workflow with GitHub Desktop App
* Additional help documentation: [Getting started with GitHub Desktop](https://help.github.com/desktop/guides/getting-started-with-github-desktop/)
* Git/GitHub link from [FH Biomedical Data Science Wiki](https://sciwiki.fredhutch.org/scicomputing/software_managecode/)
* [RStudio + Git](https://support.rstudio.com/hc/en-us/articles/200532077-Version-Control-with-Git-and-SVN)
* Challenge: BREAK until 1:43
* create a new file in your project directory named analysis.txt . Add a line of content, commit to repo.
* make a change to both analysis.txt and notes.txt . Commit both changes at once.
* Create a new folder called data . What happens when you try to commit an empty folder.

## Class 2: publishing code and collaborating with GitHub
* [backup repo](https://www.dropbox.com/s/bonwn88y1j8iwlc/first_repository.zip?dl=0): if you don't have yours from the previous class, download and unzip this repository (it includes the changes tracked in Git by the instructor in the previous class)
* [fredhutch GitHub organization](https://github.com/FredHutch)
* example repository: [this course](https://github.com/fredhutchio/git_github_intro)
* example repository: [research](https://github.com/rasilab/machkovech_2018)
* [GitHub flavored markdown](https://guides.github.com/features/mastering-markdown/)
* [guacamole](https://github.com/fredhutchio/guacamole) repository
* [Wiki link for GitHub at Fred Hutch](https://sciwiki.fredhutch.org/scicomputing/software_managecode/)
* [GitHub vs GitLab](https://svitla.com/blog/gitlab-vs-github)
* Interested in contributing to a collaborative project?
* [Wiki](https://github.com/FredHutch/wiki)
* [Coop blog](https://github.com/FredHutch/coop)

## Class 3 (optional): git command line interface
* [reference for git command line](http://swcarpentry.github.io/git-novice/reference.html)
* example data analysis repository: https://github.com/fredhutchio/example_analysis_repo
* dealing with sensitive information: https://help.github.com/en/articles/removing-sensitive-data-from-a-repository

## Resources for continued learning
* Learn about other courses through fredhutch.io [here](http://www.fredhutch.io/resources/)
* The Fred Hutch Bioinformatics and Data Science Cooperative, or Coop, hosts many community meetings and office hours about data science. Learn more information about these groups [here](https://sciwiki.fredhutch.org/scicomputing/reference_training/)
* Join the [Coop Community Slack](https://join.slack.com/t/fhbig/shared_invite/enQtMzUyMDIxNzk3MDU3LWE5NGUyMTY1NGU0N2VmMmEyNTM5YzM1MmNlMTk2YmM1OWNkMmJiNTQxMTQ4OTNkMTFjMjk3M2Q0MzkwYzQ3NDA) to talk about data science with other Hutch researchers!
* The [Fred Hutch Biomedical Data Science Wiki](https://sciwiki.fredhutch.org) is written by Hutch researchers and staff, and is a great place to find information about data management, bioinformatics, computing, and more.

###### tags: `fredhutch.io` `git`