HMSBootCamp

Setup

Frequent GitHub and command line users can skip to the "Starting the Assignment" section. Once finished, see the file titled specification.md for the assignment specification.

Command Line Basics

The command line is a text-based means of interacting with your computer. For the purposes of this bootcamp, it will allow you to navigate your folders (i.e. file directories) and utilize a program called git for version control. The following are basic commands you can use to get around the command line.

• ls "lists" files and directories directly inside the current directory
• cd [folder-name] "change directory" to the given path (relative to the current working directory)
• cd .. move up 1 step to the parent directory from the current directory
• pwd "print working directory" displays the full file path to the current directory

Installing Git

Git is a program used for version control. For the purposes of this bootcamp, you will use it to track changes you make to your files/code. See instructions below for your operating system.

• MacOS
  • Opening Terminal will allow you to access the command line interface for your computer
  • GOOD NEWS: You probably already have git installed! Move on for now and reference the following bullet if you see git: command not found when trying to use a git command
  • Open the Terminal app and type in xcode-select -install to install a suite of useful tools for programming, including git
• Windows
  • Install git from the official link
  • Opening Git Bash will allow you to access the command line interface on your computer

At this point, open Terminal on MacOS or Git Bash on Windows and just try to navigate within a commonly used directory (e.g. Documents) using command line commands listed above!

Connecting to GitHub

1. Sign up for a free GitHub account with this link.
2. Open Git Bash
3. Paste the following text into your command line ssh-keygen -t rsa -b 4096 -C "your_email@example.com" and LEAVE THE FILE AND PASSPHRASE BLANK! Just hit enter for both.
4. Copy this unique key to your computer's clipboard by running...
   1. Windows: cat ~/.ssh/id_rsa.pub | clip
   2. MacOS: pbcopy < ~/.ssh/id_rsa.pub
5. Navigate to your keys page and click New SSH key
   1. Paste into the Key text box
   2. Write a title for the key (e.g. bootcampkey) in the Title text box
6. Confirm correct setup of the key by running ssh -T git@github.com and see official GitHub documentation for the following steps.

Setup adapted from official GitHub documentation, feel free to follow these steps if you would like to do so instead

Cloning Into Your Own Repository

1. Create a new repository at github.com by clicking the green New button.

   1. Fill in the Repository name box with: HMSBootCamp
   2. You may make the repository public
   3. DO NOT check Add a README file
   4. Click Create Repository

2. Use the command line in your Terminal (MacOS) or Git Bash (Windows) to navigate to a directory you want to store this assignment's folder in (e.g. Documents), run git clone git@github.com/mbi6245/HMSBootCamp.git in the command line.

   TIP: refer to the above "Command Line" for instructions on how to cd into your desired directory

3. Run cd HMSBootCamp

4. Run git remote rename origin upstream

5. Run git remote add origin https://github.com/YOUR-ACCOUNT/HMSBootCamp.git

6. Run git push origin main

Adapted from this stackoverflow post, feel free to follow these steps if you would like to do so instead

Installing R/RStudio and Starting the Assignment

1. Navigate to the official RStudio website and scroll down to the DOWNLOAD AND INSTALL R and DOWNLOAD RSTUDIO DESKTOP buttons; click both

2. Run the downloaded R language installer; you should just accept all default options by continuing to hit the Next buttons until you reach Finish or Install

3. Run the downloaded RStudio installer; you should also just accept all default options by continuing to hit the Next buttons until you reach Finish or Install

4. Open Rstudio and hit the drop down menu in the top left of your screen pictured below to create a new .Rmd file (you may be prompted to install some packages, please do so) titled Data_Analysis

   

5. Ensure that the new .Rmd file is in the HMSBootCamp directory you created above by saving the file (CTRL + s for Windows or Cmd + s for MacOS) and clicking on the correct folder in the graphical user interface.

6. See specification.md for next steps