University of Arizona

Oct 26-27, 2019

8:30 am - 5:00 pm

Instructors: Noah Nelson, Sateesh Peri, Kelsey Gonzalez, Xue Pan, Travis Struck, Uwe Hilgert

Helpers: Drake Asberry, Brian Bell, Jennifer Kadowaki, David LeBauer, Torbet McNeil, Erica Newman, Cristian Palacios, Adriana Picoral, Fernando Rios, Austin Rutherford, Saren Seeley, Marnee Dearman

Apply for the workshop at http://bit.ly/356EkJl.

General Information

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, including program design, version control, data management, and task automation. 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: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Please check your email for the workshop location!. Get directions with OpenStreetMap or Google Maps.

When: Oct 26-27, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

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

Accessibility: We are committed to making this workshop accessible to anyone. The workshop organisers have checked that:

Links to workshop materials will be provided below. If we can provide additional resources to help making learning easier for you (e.g. large-font hand-outs, sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email hilgert@bio5.org for more information.


Surveys

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

Pre-workshop Survey

Post-workshop Survey


Schedule

Saturday October 26

08:30 Automate tasks with the Unix shell and git/GitHub
10:30 Coffee
12:00 Lunch break
13:00 Unix shell/git/GitHub, cont.
14:45 Coffee
15:00 Scientific Analyses with R and git/GitHub
17:00 End of Day

Sunday October 27

08:30 Scientific Analyses with R and git/GitHub, cont.
10:30 Coffee
12:00 Lunch break
13:00 R/R-Studio/git/GitHub, cont.
14:45 Coffee
17:00 End of Day

Schedule subject to change if necessary.


Syllabus

Syllabus & Learning Objectives

Take control with the Unix Shell

  • Work in vs. work below the GUI
  • Navigate the shell
  • Find, create, copy, move and delete folders and files
  • Shell over GUI: Command history and tab completion
  • Connect commands into workflows: pipes and redirection
  • Automate repetitive tasks: loops
  • Save and run workflows in scripts
Resources:

Write analysis programs in R

  • Work with vectors and data frames
  • Read and plot data
  • Create and use functions
  • Create loops and conditionals
  • Use R from the command line
Resources:

Collaborate with git/GitHub

  • Access a repository and pull files
  • Create a repository
  • Record changes: add, commit, ...
  • View changes: status, diff, ...
  • Ignore files
  • Work on the web: clone, pull, push, ...
  • Resolve conflicts
Resources:


Computer Preparation

To participate in the Software Carpentry workshop, you will need access to the software described below. Unless you prepare your laptop as described below you will be unable to follow along. In addition, you will need an up-to-date web browser, we recommend Firefox, Chrome or Safari as Internet Explorer/Edge can be buggy.

Should you encounter issues while installing the software below, please look for a solution in our Configuration Problems and Solutions wiki page. If even this does not help, please get in touch with us using contact details above and we will attempt to provide a solution.


The Bash Shell (a.k.a. Command Line/Shell/Unix)

Bash is a commonly-used shell (= Unix command language) that gives you the power to quickly do simple tasks on your computer. Bash stands for 'Bourne Again Shell'; if you are interested in the history of the term and the underlying technological development, please search the Web for 'Bash Shell'.

Windows

  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    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 gitbash will not work properly, requiring you to remove the GitBash 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 "Enable file system caching" and "Enable Git Credential Manager" are selected and click on "Next".
    8. Click on "Install".
    9. Click on "Finish".
  3. 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.

macOS

The default shell in all versions of macOS is Bash, 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.

Linux

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.


Text Editor

Writing code is much easier with respectively optimized text editors that include features such as automatic color-coding of key words and syntax-highlighting. We will use the basic editor 'nano' in the workshop; it comes pre-installed with the git-bash download above for Windows, Mac and Linux.

Windows

Click the Start button and type 'git bash' into the search window.
Click on the "Git Bash" icon to open the shell.
Type 'nano test.txt' to open a text editor. If this does not open the nano text editor contact the workshop administrator at the email listed above.
Type 'Test'.
To exit the nano editor press Ctrl and type 'x' (a.k.a. '^X'; additional commands are listed at the bottom of the text edito window.

macOS

During the workshop we will be using the basic editor nano. nano should be pre-installed; see the Git installation video tutorial for an example on how to open nano.

Linux

During the workshop we will be using the basic editor nano. nano should be pre-installed


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 (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

For the workshop you will need a GitHub account, if you don't have one already please get it at github.com. Basic GitHub accounts are free. However, 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 at GitHub.

Windows

Git should be installed on your computer as part of your Bash install (described above).

macOS

For OS X 10.9 and higher, 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.

Linux

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.


R

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

Windows

Video Tutorial

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.

macOS

Video Tutorial

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

Linux

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