Fork me on GitHub

iPlant Collaborative, University of Arizona

Feb 21-22, 2015

9:00 am - 4:30 pm

Instructors: Naupaka Zimmerman, Jonathan Strootman

Helpers: Blake Joyce, Joshua D. Lioi, John McMullin, Andre Mercer, Uwe Hilgert

General Information

Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This two-day hands-on workshop will cover basic concepts and tools; participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Who: The course is aimed at postdocs, graduate students, and other researchers.

Where: Manuel Pacheco Integrated Learning Center Room 119, 1500 E University Blvd, Tucson, AZ 85719. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct. In order to use iPlant resources participants are advised to register for an iPlant account. Users should specifically request access to 'Atmosphere' when they register. Participants should also register for a Github account. Users will also have to be registered on the UA campus network to have access to WiFi.

Contact: Please mail or for more information. If you are having issues with iPlant account registration, please mail

Registration: A $25 registration fee covers refreshments, lunches and instruction for the workshop. Priority goes to practicing UA researchers as outlined above. Undergraduate students and non-UA participants can be admitted upon special request. Registration is is done through eventrbrite, linked on this page (see above).

Surveys: Each Software Carpentry workshop is unique, and the instructors do adjust the workshop to best suit the needs of the participants. To those of you who filled out the pre-workshop survery, thank you.
Please take some time to fill out a post-workshop survey. post-workshop skills survey. Data gathered using this survey is for internal (and instructor) use only and will be anonymized if distributed externally.


Day 1

09:00 Intro to scripting and analysis in R
10:30 Coffee break
12:00 Lunch break
13:00 Getting around and automating tasks in the shell
14:30 Coffee break
16:00 Wrap-up

Day 2

09:00 Version control with Git
10:30 Coffee break
12:00 Lunch break
13:00 Data munging and visualization with ggplot and R. Final exercise with ggplot and knitr available here.
14:30 Coffee break
16:00 Wrap-up

Summary and Reference

The Unix Shell

  • Files and directories: pwd, cd, ls, mkdir, ...
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things: grep, find, ...
  • Reference...

Programming in R

  • Working with vectors and data frames
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals: for, if, else
  • Using R from the command line
  • Reference...

Version Control with Git

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files
  • Working on the web: clone, pull, push, ...
  • Resolving conflicts
  • Open licenses
  • Where to host work, and why
  • Reference...


To participate in a Software Carpentry workshop, you will need working copies of the software described below.
Additionally, you will need a Github account and an iPlant account.
Please make sure to install everything (or at least to download the installers) and complete your user registrations before the start of your workshop.


Github User Account

If you don't already have a Github account, please visit and create one. Be sure to remember which email address you use, you'll need it later ;)

iPlant Collaborative User Account

If you haven't already done so, visit the iPlant user portal at to setup your account. When registering, be sure to use a .edu email address!
Once you have registered, log in to the iPlant user portal and request access to Atmosphere.
For more information about iPlant, please visting the website at


When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by ':q!' (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

The Bash Shell

Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.


Git is a state-of-the-art version control system. It lets you track who made changes to what when and has options for easily updating a shared or public version of your code on


R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we will use RStudio, an interactive development environment (IDE).


Git Bash

Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.

Software Carpentry Installer

This installer requires an active internet connection

After installing Git Bash:

  • Download the installer.
  • If the file opens directly in the browser select File→Save Page As to download it to your computer.
  • Double click on the file to run it.


nano is the editor installed by the Software Carpentry Installer, it is a basic editor integrated into the lesson material.

Notepad++ is a popular free code editor for Windows. Be aware that you must add its installation directory to your system path in order to launch it from the command line (or have other tools like Git launch it for you). Please ask your instructor to help you do this.


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

Mac OS X


The default shell in all versions of Mac OS X is bash, so no need to install anything. You access bash from the Terminal (found in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.


We recommend Text Wrangler or Sublime Text. In a pinch, you can use nano, which should be pre-installed.


For OS X 10.8 and higher, install Git for Mac by downloading and running the installer. For older versions of OS X (10.5-10.7) use the most recent available installer for your OS available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.


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



The default shell is usually bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.


If Git is not already available on your machine you can try to install it via your distro's package manager (e.g. apt-get or yum).


Kate is one option for Linux users. In a pinch, you can use nano, which should be pre-installed.


You can download the binary files for your distribution from CRAN. Or you can use your package manager, e.g. for Debian/Ubuntu run apt-get install r-base or yum install R. Also, please install the RStudio IDE.

All operating systems