UCSD Carpentries Bootcamp: R, Unix Shell, & Git

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools used with the R programming language and version control with Git. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: This workshop is open to UCSD students, staff, and faculty.

You don't need to have any previous knowledge of programming or the tools presented in the workshop to attend. A laptop is required for each session.

Where: Virtual (via Zoom).

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).

Contact: Please mail kkt008@ucsd.edu or rotsuji@ucsd.edu for more information.

Assessment: A Co-Curricular of Record activity recognition will be given to the student who:

Attend and participate in all sessions
Pass the post-workshop quizz

For more information on the UC San Diego Co-Curricular of Record (CCR), please visit the UCSD Engaged Learning Tools Co-Curricular Record page.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

Date	Session	Topics
Oct 10	Introduction to R - Session 1	Intro to R & RStudio - basics, data structures, and data import/export
Oct 11	Introduction to R - Session 2	dplyr and tidyverse
Oct 12	Introduction to R - Session 3	Plotting with ggplot2 and knitr
Oct 13	Unix Shell & Version Control w/ Git	Unix Shell: Introduction, Navigating the file system, & working with files & directories Git: Introduction, Creating a Repository, Tracking Changes, and Collaborating

Curriculum

For this workshop we will be referencing the R for Reproducible Scientific Analysis, The UNIX Shell, and Version Control with Git Carpentries curricula.

Data

We will be using the 5 year gapminder data, feline data, and shell lesson data. You can go ahead and set up a RStudio project and download the data following these instructions. The data downloads are as follows: Gapminder data, feline data, and the shell-lesson data.

Collaborative Notes

We will use HackMD collaborative notes for taking notes, and sharing URLs and bits of code. Use the following link to access the collaborative notes: https://hackmd.io/@kkt008/r1niQyFzo

Setup

To participate in this workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

Video Tutorial: SWC R Install Windows

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Video Tutorial: SWC R Install Mac

Instructions for R installation on various Linux platforms (debian, fedora, redhat, and ubuntu) can be found at . These will instruct you to use your package manager (e.g. for Fedora run sudo dnf install R and for Debian/Ubuntu, add a ppa repository and then run sudo apt-get install r-base). Also, please install the RStudio IDE.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do tasks more quickly.

Download the Git for Windows installer.
Run the installer and follow the steps below:
1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
2. From the dropdown menu select "Use the nano editor by default" and click on "Next".
3. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
4. Ensure that "Use the native Windows Secure Channel library" is selected and click on "Next".
5. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
6. Ensure that "Use Windows' default console window" is selected and click on "Next".
7. Ensure that "Default (fast-forward or merge) is selected and click "Next"
8. Ensure that "Enable file system caching" and "Enable Git Credential Manager" are selected and click on "Next".
9. Click on "Install".
10. Click on "Finish" or "Next".
If your "HOME" environment variable is not set (or you don't know what this is):
1. Open command prompt (Open Start Menu then type cmd and press Enter)
2. Type the following line into the command prompt window exactly as shown:
  setx HOME "%USERPROFILE%"
3. Press Enter, you should see SUCCESS: Specified value was saved.
4. Quit command prompt by typing exit then pressing Enter

This will provide you with both Git and Bash in the Git Bash program.

Video Tutorial: Windows Installation

The default shell in some versions of macOS is Bash, and Bash is available in all versions, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

To see if your default shell is Bash type echo $SHELL in Terminal and press the Return key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash

If you want to change your default shell, see this Apple Support article and follow the instructions on "How to change your default shell".

Video Tutorial MacOS Installation

The default shell is usually Bash and there is usually no need to install anything.

To see if your default shell is Bash type echo $SHELL in a terminal and press the Enter key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Git should be installed on your computer as part of your Bash install (see the Shell installation instructions).

For macOS, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

Video Tutorial: SWC Install Shell, Git, and Nano on Mac

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.