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Carpentries @ Oklahoma State University: Workshop Resources
Information about Data and Software Carpentries workshops and the Carpentries community
Workshop Software
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) and an up to date browser. They are also required to abide by The Carpentry's Code of Conduct.
Workshops may be held in the Library's computer instruction lab or online via Zoom, but it is advisable to use a personal device so that the tools are available to use following the workshop. Instructors are available 30 minutes before the start of each workshop to assist if you have problems.
Software Carpentry participants should install the following OR additional software as detailed in the pre-workshop email:
- Bash (Unix Shell)
- Git
- Python AND Jupyter Notebook
Data Carpentry participants should install each of the following OR as detailed in the pre-workshop email:
- Text Editor
- SQL
- R AND R Studio
- OpenRefine
Find more specific information below on how to download and install required software for the workshop you are attending.
Access reference guides for various software tools here.
Software Installation Instructions
Updated 1/11/19
Jump to the installation instructions depending on your software needs:
The Bash Shell
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
Windows
Video Tutorial- Download the Git for Windows installer.
- Run the installer and follow the steps below:
- 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.
- Select “Use the nano editor by default” and click on “Next”.
- Keep "Use Git from the Windows Command Prompt" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
- Click on "Next".
- Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
- Select "Use Windows' default console window" and click on "Next".
- Click on "Install".
- Click on "Finish".
- If your "HOME" environment variable is not set (or you don't know what this is):
- Open command prompt (Open Start Menu then type
cmd
and press [Enter]) - Type the following line into the command prompt window exactly as shown:
setx HOME "%USERPROFILE%"
- Press [Enter], you should see
SUCCESS: Specified value was saved.
- Quit command prompt by typing
exit
then pressing [Enter]
- Open command prompt (Open Start Menu then type
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.
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.
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
.
Text Editor
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 macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.
Windows
nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.
Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.
macOS
nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.
Others editors that you can use are BBEdit or Sublime Text.
Linux
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.
Others editors that you can use are Gedit, Kate or Sublime Text.
Python
Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.
Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).
We will teach Python using the Jupyter notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).
Windows
-
Open this link with your web browser.
-
Download the Python 3 installer for Windows.
-
Install Python 3 using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.
macOS
-
Open this link with your web browser.
-
Download the Python 3 installer for OS X.
-
Install Python 3 using all of the defaults for installation.
Linux
-
Open this link with your web browser.
-
Download the Python 3 installer for Linux.
(The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.) -
Open a terminal window.
-
Type
bash Anaconda3-
and then press Tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with:
cd Downloads
Then, try again.
-
Press Return. You will follow the text-only prompts. To move through the text, press Spacebar. Type
yes
and press enter to approve the license. Press enter to approve the default location for the files. Typeyes
and press enter to prepend Anaconda to yourPATH
(this makes the Anaconda distribution the default Python). -
Close the terminal window.
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
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
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.
SQLite
SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.
Windows
The Data Carpentry Windows Installer installs SQLite for Windows. If you used the installer to configure nano, you don't need to run it again.
macOS
SQLite comes pre-installed on macOS.
Linux
SQLite comes pre-installed on Linux.
If you installed Anaconda, it also has a copy of SQLite without support to readline
. Instructors will provide a workaround for it if needed.
OpenRefine
For this lesson you will need OpenRefine and a web browser. Note: this is a Java program that runs on your machine (not in the cloud). It runs inside a web browser, but no web connection is needed.
Windows
Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It will not run correctly in Internet Explorer.
Download software from http://openrefine.org/
Create a new directory called OpenRefine.
Unzip the downloaded file into the OpenRefine directory by right-clicking and selecting "Extract ...".
Go to your newly created OpenRefine directory.
Launch OpenRefine by clicking openrefine.exe
(this will launch a command prompt window, but you can ignore that - just wait for OpenRefine to open in the browser).
If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.
Mac
Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It may not run correctly in Safari.
Download software from http://openrefine.org/.
Create a new directory called OpenRefine.
Unzip the downloaded file into the OpenRefine directory by double-clicking it.
Go to your newly created OpenRefine directory.
Launch OpenRefine by dragging the icon into the Applications folder.
Use Ctrl-click/Open ...
to launch it.
If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.
Linux
Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser.
Download software from http://openrefine.org/.
Make a directory called OpenRefine.
Unzip the downloaded file into the OpenRefine directory.
Go to your newly created OpenRefine directory.
Launch OpenRefine by entering ./refine
into the terminal within the OpenRefine directory.
If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.
Copyright © 2016–2018 Software Carpentry
Fast Reference for Carpentry Software Tools
- R for Data ScienceA complete reference for using R to analyze, visualize and manage data. Available as either a downloadable pdf or a hardcopy book for purchase.
- Basic Operations in RProgramming with R
- A cheat sheet for Unix Shell (Bash)Commands and reminders for using Bash
- Plotting with PythonCommands and shortcuts for plotting and programming in Python
- Programming with PythonGlossary of Python commands
- R for Reproducible Scientific AnalysisKey points for using R and R Studio
- Version Control with GitGit cheatsheets