Data Carpentry Workshop Setup Instructions

Requirements: Data Carpentry's teaching is hands-on, so participants are encouraged to bring in and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop. (We will provide instructions on setting up the required software several days in advance) There are no pre-requisites, and we will assume no prior knowledge about the tools.

Contact: Please email admin@datacarpentry.org for questions and information not covered here.

Setup

To participate in a Data Carpentry workshop, you will need 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 your workshop. If you run into any problems, please feel free to email the instructor or arrive early to your workshop on the first day. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

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. Python & Jupyter notebooks
    In the workshop, we will be using Jupyter notebooks to access the Python environment. You can install both Python and Jupyter notebooks from a single install.
    • Follow the Anaconda link hereto the Anaconda website. There are versions of Anaconda available for Windows, macOS and Linux. The web site will detect your operating system and provide a link to the appropriate download.
    • There will be two options, one for Python 2.x and another for Python 3.x. We will take the Python 3.x option.
    • For Windows and Linux there is the option of either a 64 bit (default) download or a 32bit download. Unless you know that you do not have an old 32bit pc you should choose the 64bit installer.
    • Run the downloaded installer program. Accept the default settings until you are given the option to add Anaconda to your environmental Path variable. Despite the recommendation not to and the subsequent warning, you should select this option. This will make it easier later on to start Jupyter notebooks from any location.
    • The installation can take a few minutes. When finished you should be able to open a cmd prompt (Type cmd from Windows start) and into the cmd window type 'python'.
    • You should get a message sayingwhat version of Python you installed and a '>>>' prompt.
    • You can close the python session by typing 'quit()'.
    • You can check Jupyter by typing 'Jupyter notebook'. This will produce a variety of messages, but more importantly, it should load the Jupyter front page in your default browser.
    • If your browser doesn't open, open it manually and type in 'localhost:8888' as the URL

  4. SQLite
    For this workshop we're going to use the free application DB Browser for SQLite
    • The software can be downloaded from the DB Browser site
    • Select the latest Windows version and download the single installer file.
    • Execute the downloaded file by double clicking it.
    • You will require admin permissions to perform the install.
    • Accept all of the default options in the installation wizard.
    • The installation does not create a desktop icon. You can find/run DB Browser from the Windows search/start button.

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.
    • 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. SQLite
    For this workshop we're going to use the Firefox SQLite Plugin. It works through the web browser Firefox.
    • If you don't already have Firefox installed install Firefox
    • Start Firefox
    • Go to the plugin homepage.
    • Click the "Add Now" button.
    • Click "Install Now" on the dialog that appears after the download completes.
    • Restart Firefox when prompted.
    • Select "SQLite Manager" from the "Tools" menu and it will open within Firefox

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. Python & Jupyter notebooks
    In the workshop, we will be using Jupyter notebooks to access the Python environment. You can install both Python and Jupyter notebooks from a single install.
    • Follow the Anaconda link hereto the Anaconda website. There are versions of Anaconda available for Windows, macOS and Linux. The web site will detect your operating system and provide a link to the appropriate download.
    • There will be two options, one for Python 2.x and another for Python 3.x. We will take the Python 3.x option.
    • For Windows and Linux there is the option of either a 64 bit (default) download or a 32bit download. Unless you know that you do not have an old 32bit pc you should choose the 64bit installer.
    • Run the downloaded installer program. Accept the default settings until you are given the option to add Anaconda to your environmental Path variable. Despite the recommendation not to and the subsequent warning, you should select this option. This will make it easier later on to start Jupyter notebooks from any location.
    • The installation can take a few minutes. When finished you should be able to open a terminal window and 'python'.
    • You should get a message saying what version of Python you installed and a '>>>' prompt.
    • You can close the python session by typing 'quit()'.
    • You can check Jupyter by typing 'jupyter notebook'. This will produce a variety of messages, but more importantly, it should load the Jupyter front page in your default browser.
    • If your browser doesn't open, open it manually and type in 'localhost:8888' as the URL

  4. SQLite
    For this workshop we're going to use the free application DB Browser for SQLite
    • The software can be downloaded from the DB Browser site
    • Instructions for installing DB Browser for various flavours of Linux are given on the page.
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