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 collin.storlie@jcu.edu.au 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.

Platform-specific Notes

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 Download Version 4.4.2. 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. Putty
    You will need a terminal program to access the AWS Cloud/HPC cluster.
    • Go to the Putty download page
    • Click on putty.exe link to download the install file
    • To use it, double-click on the downloaded file
    • Follow any installation instructions, if any

  3. FTP Client (Filezilla)
    An FTP client will help you transfer files easily between your computer and the cloud.
    • Go to the Filezila download page
    • Chose the download link appropriate to your system
    • To use it, double-click on the downloaded file
    • Follow any installation instructions, if any
    • At the workshop we will give you additional information (e.g. host, username, port) to connect

  4. Remote Desktop Client (VNC Viewer)
    A Remote Desktop Client allows you to interact with a Remote Computer through a GUI interface.
    • Go to the VNC Viewer download page
    • Chose the download link appropriate to your system
    • To use it, double-click on the downloaded file

  5. 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.
    • 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
    • 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.

  6. IGV
    If time permits, we will use The Broad Institute's IGV (Integrated Genome Viewer) for looking at SAM and BAM files, SNPs, and variant calls.
    • To download IGV, please visit this page and log in. Please register if you do not already have a login.
    • Click on the large button for the Download Binary Distribution
    • Find the zip archive on your computer and expand it
    • To run IGV, double-click on the IGV.bat file.

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 Download Version 4.4.2. 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. FTP Client (Filezilla)
    An FTP client will help you transfer files easily between your computer and the cloud.
    • Go to the Filezila download page
    • Chose the download link appropriate to your system
    • To use it, double-click on the downloaded file
    • Follow any installation instructions, if any
    • At the workshop we will give you additional information (e.g. host, username, port) to connect

  3. Remote Desktop Client (VNC Viewer)
    A Remote Desktop Client allows you to interact with a Remote Computer through a GUI interface.
    • Go to the VNC Viewer download page
    • Chose the download link appropriate to your system
    • To use it, double click the .dmg file and then drag & drop into Applications.

  4. 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 0.98.1103 - 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.

  5. IGV
    If time permits, we will use The Broad Institute's IGV (Integrated Genome Viewer) for looking at SAM and BAM files, SNPs, and variant calls.
    • To download IGV, please visit this page and log in. Please register if you do not already have a login.
    • Click on the large button for the Download Binary Distribution
    • Find the zip archive on your computer and expand it
    • To run IGV, double-click on the IGV.bat file.

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. 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 Linux should automatically be selected. Click Download Version 4.4.2. 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. FTP Client (Filezilla)
    An FTP client will help you transfer files easily between your computer and the cloud.
    • Go to the Filezila download page
    • Chose the download link appropriate to your system
    • To use it, double-click on the downloaded file
    • Follow any installation instructions, if any
    • At the workshop we will give you additional information (e.g. host, username, port) to connect

  3. Remote Desktop Client (VNC Viewer)
    A Remote Desktop Client allows you to interact with a Remote Computer through a GUI interface.
    • Go to the VNC Viewer download page
    • Chose the download link appropriate to your system
    • To use it, double click the .dmg file and then drag & drop into Applications.

  4. IGV
    If time permits, we will use The Broad Institute's IGV (Integrated Genome Viewer) for looking at SAM and BAM files, SNPs, and variant calls.
    • To download IGV, please visit this page and log in. Please register if you do not already have a login.
    • Click on the large button for the Download Binary Distribution
    • Find the zip archive on your computer and expand it
    • To run IGV, double-click on the IGV.bat file.

  5. 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.
    • R is available through most Linux package managers. 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 yum install R).
    • To install RStudi, 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
    • Once it's installed, open RStudio to make sure it works and you don't get any error messages.

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