Data Carpentry Workshop Setup Instructions

Requirements: Data Carpentry's teaching is hands-on, so participants are expected to bring in and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop. There are no pre-requisites, and we will assume no prior knowledge about the tools.

Contact: Please email szamosjc@mcmaster.ca for questions and information not covered here.

Setup

To participate in a Data Carpentry workshop, you will need the data files and working copies of the software described below. Please make sure to install everything and try opening it to make sure it works before the start of the workshop. If you run into any problems, please come to our software installation party (date and location TBD). Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

Data

We recommend creating a directory (folder) on your computer for workshop materials. You can download all files into that directory and then work in there for the workshop itself. The files you'll need to download are:

Software

This workshop will be using the software outlined in the install instructions below. Please see the section for your operating system for those directions.

Windows

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they're working. If you have any problems, don't hesitate to email the instructors to ask for help, or arrive early on the first day of the workshop to get help.

  1. A spreadsheet program
    For this workshop you will need a spreadsheet program. Many people already have Microsoft Excel installed, and if you do, you're set!
    If you need a spreadsheet program, there are a few other options, like OpenOffice and LibreOffice. Install instructions for LibreOffice, which is free and open source, are here.
    • Download the Installer
      Install LibreOffice by going to the installation page. The version for Windows should automatically be selected. Click on the button below "Main Installer" Download Version x.y.z. You will go to a page that asks about a donation, but you don't need to make one. Your download should begin automatically.
    • Install LibreOffice
      Once the installer is downloaded, double click on it and it should install.
    • To use LibreOffice, double click on the icon and it will open.

  2. OpenRefine
    OpenRefine (previously Google Refine) is a tool for data cleaning that runs through a web browser, and any browser - Safari, Firefox, Chrome, Explorer - should work fine. You will need to download OpenRefine and install it, and when you open it, it will run through the browser, but you don't need an internet connection, and the data will all be stored on your computer.
    • Go to the OpenRefine download page
    • Click on Windows kit to download the install file
    • To use it, unzip, and double-click on openrefine.exe (if you're having issues with openrefine.exe try refine.bat instead)
    • OpenRefine will then open in your web browser.
    • If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.

  3. R
    In the workshop, we will use RStudio. RStudio is a nice interface to the programming language R. To use RStudio, you need to install both R and RStudio. If you have previously installed R and/or RStudio, please make sure if at all possible that you have the most up-to-date versions.
    • Download R from here
    • Run the .exe file that was just downloaded
    • Go to the RStudio Download page
    • Under Installers select RStudio 0.98.1103 - Windows XP/Vista/7/8/10
    • Double click the file to install it
    • Once it's installed, open RStudio to make sure it works and you don't get any error messages.

  4. Git and GitHub Desktop
    • 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.
    • Download the Git for Windows installer.
    • Run the installer and follow the steps bellow. If there is a step not mentioned here, please leave the default settings:
      1. Click on "Next".
      2. Click on "Next".
      3. 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.
      4. Click on "Next".
      5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
      6. Keep "Use Windows' default console window" selected and click on "Next".
      7. Click on "Install".
      8. Click on "Finish".
    • Download the Github Desktop executable and double-click to run it.

Mac

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they're working. If you have any problems, don't hesitate to email the instructors to ask for help, or arrive early on the first day of the workshop to get help.

  1. A spreadsheet program
    For this workshop you will need a spreadsheet program. Many people already have Microsoft Excel installed, and if you do, you're set!
    If you need a spreadsheet program, there are a few other options, like OpenOffice and LibreOffice. Install instructions for LibreOffice, which is free and open source, are here.
    • Download the Installer
      Install LibreOffice by going to the installation page. The version for Mac should automatically be selected. Click on the button below "Main Installer" Download Version x.y.z. You will go to a page that asks about a donation, but you don't need to make one. Your download should begin automatically.
    • Install LibreOffice
      Once the installer is downloaded, double click on it and it should install.
    • To use LibreOffice, double click on the icon and it will open.

  2. OpenRefine
    OpenRefine (previously Google Refine) is a tool for data cleaning that runs through a web browser, and any browser - Safari, Firefox, Chrome, Explorer - should work fine. You will need to download Google Refine and install it, and when you open it, it will run through the browser, but you don't need an internet connection, and the data will all be stored on your computer.
    • Go to the OpenRefine download page
    • Click on Mac kit to download the install file
    • Open the downloaded .dmg file
    • Drag the icon in to the Applications folder
    • Double click on the icon and Google Refine will then open in your web browser.
    • If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.

  3. R
    In the workshop, we will use RStudio. RStudio is a nice interface to the programming language R. To use RStudio, you need to install both R and RStudio. If you have previously installed R and/or RStudio, please make sure if at all possible that you have the most up-to-date versions.
    • Go to CRAN and click on Download R for (Mac) OS X
    • Select the .pkg file for the version of OS X that you have and the file will download.
    • Double click on the file that was downloaded and R will install
    • Go to the RStudio Download page
    • Under Installers select RStudio x.yy.zzz - Mac OS X 10.6+ (64-bit) to download it.
    • Once it's downloaded, double click the file to install it
    • Once it's installed, open RStudio to make sure it works and you don't get any error messages.

  4. Git and GitHub Desktop
    • 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.
    • For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. 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.
    • Download Github Desktop
    • Unzip the .zip file
    • You can copy the program to your Applications/ folder, or run it from wherever you unzipped it

Linux

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they're working. If you have any problems, don't hesitate to email the instructors to ask for help, or arrive early on the first day of the workshop to get help.

  1. A spreadsheet program
    For this workshop you will need a spreadsheet program. LibreOffice comes preinstalled with several Linux distributions. If you don't already have it, use your package manager to install it: (e.g., sudo apt-get install libreoffice for Ubuntu and other Debian-based distributions).

  2. OpenRefine
    OpenRefine (previously Google Refine) is a tool for data cleaning that runs through a web browser, and any browser - Safari, Firefox, Chrome, Explorer - should work fine. You will need to download Google Refine and install it, and when you open it, it will run through the browser, but you don't need an internet connection, and the data will all be stored on your computer.
    • Go to the OpenRefine download page
    • Click on Linux kit to download the install file
    • Download and extract
    • Type ./refine in your terminal and Google Refine will then open in your web browser.
    • If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.

  3. R
    In the workshop, we will use RStudio. RStudio is a nice interface to the programming language R. To use RStudio, you need to install both R and RStudio. If you have previously installed R and/or RStudio, please make sure if at all possible that you have the most up-to-date versions.
    • Follow the instructions for your distribution from CRAN. For most distributions, you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base, and for Fedora run sudo yum install R) but make sure that you have at least R 3.2.2 (as pre-packaged versions might be out of date).
    • To install RStudio, go to the RStudio Download page
    • Under Installers select the version for your distribution.
    • Once it's downloaded, double click the file to install it (or sudo dpkg -i rstudio-x.yy.zzz-amd64.deb at the terminal).
    • Once it's installed, open RStudio to make sure it works and you don't get any error messages.

  4. Git and Github Desktop
    • 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 is likely to have been included in your original install, but if it was not you can use your package manager to install it (e.g. sudo apt-get install git on Debian-based systems like Ubuntu).
    • Github desktop is not officially released for Linux, but there is a port available here. You can use your package manager to install the .deb (Debian-based systems) or .rpm (Red Hat-based systems) files, or compile and install from source.
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