Overview

Editor

When you're writing scripts or text, 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. (This will lose any unsaved changes to the file.)

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.

R

R is a programming language that specializes in statistical computing. It is a powerful tool for exploratory data analysis. To interact with R, we will use RStudio, an interactive development environment (IDE).

SQL

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite, either directly or through a browser plugin.

OpenRefine

OpenRefine (formerly Google Refine) is a powerful tool for exploring and working with messy data.

Windows

Editor

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.

Git Bash

Install Git (version control) and a Bash shell for Windows from the msysGit project's homepage. This will provide you with Bash in the Git Bash program.

Software Carpentry Installer

Other tools used in Data Carpentry have been packaged up by Software Carpentry in an installer. This installer requires an active internet connection.

R

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

SQLite

Install the Firefox SQLite browser plugin described below.

OpenRefine

Download the OpenRefine software described below.

Mac OS X

Bash

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.

Editor

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

R

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

SQLite

sqlite3 comes pre-installed on Mac OS X. Also install the Firefox SQLite browser plugin described below.

OpenRefine

Download the OpenRefine software described below.

Linux

Bash

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.

Editor

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

R

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. Also, please install the RStudio IDE.

SQLite

sqlite3 comes pre-installed on Linux. Also install the Firefox SQLite browser plugin described below.

OpenRefine

Download the OpenRefine software described below.

Miscellaneous

Firefox SQLite Plugin

Instead of using sqlite3 from the command line, you may use this plugin for Firefox instead. To install it:

OpenRefine

Head to the OpenRefine download page for information on how to install it. It will run through a browser, but will not need to use an internet connection, and your data will also be securely stored on your own computer.