Included on the USB flash drive is the latest Ubuntu Linux distribution. We also include the WUBI installer, which is the recommended way to install Ubuntu on Windows. Our motivation is to provide a UNIX environment for participants with Windows notebooks and laptop computers. It is similar to a typical dual-boot configuration; when the computer boots up, you choose to boot into either Windows or Linux. Although WUBI does not physically partition your hard drive, it does require at least 5 GB of free disk space.

Installation Instructions

  1. On the flash drive, browse to the Ubuntu Linux folder and double-click on the install.bat file. Note: if you get an error message in a dialog box, press Cancel repeatedly — this is a bug with the WUBI installer, which you may or may not encounter. If you do get an error in a dialog box, you may have to press Cancel many, many times, but it will eventually go away and the installation will continue.
  2. You will be prompted to choose a drive on which to install Ubuntu. You will need to specify a username and password (please remember your password!), an initial amount of disk space to allocate to the Ubuntu Linux OS, and a preferred language. 
    For the Workshop on Genomics, please allocate at least 20 GB of disk space, at minimum. It will be beneficial to allocate much more than this (e.g., 50 or 100 GB) if you can afford it, as many of the analyses generate a large amount of data.) 

    Once you are confident that everything is correct you may proceed with the installation.

  3. Shortly into the installation, you will be asked to reboot your computer. After you reboot, you will encounter a menu giving you the choice to boot into Microsoft Windows or Ubuntu Linux. In order to properly continue the installation, choose Ubuntu. If you accidentally boot into Windows, simply restart your computer and try again. You will be asked to reboot one more time during the installation process.
  4. If all goes well, you will eventually be presented with a login screen. To log in, simply enter the username and password you specified at the beginning of the installation process.
  5. Note: if you have your own Linux installation, please do not run any of our Linux installation scripts as they have the potential to corrupt your installation!
  6. On the USB flash drive under Install, browse to the Linux folder. Copy the WME_install.zip file to your computer and uncompress the file. Inside the WME_install folder, double-click on the install.sh file, choose “Run in Terminal”, type your password in the terminal when prompted, and press enter. (Your password may not appear when typing!) The install script will run for several minutes – when it completes, you will automatically be logged out. Then you should log in again with your username and password. (Note – if any errors pop up in dialog boxes, please ignore them. The installation should continue in the background.)
  7. The workshop applications have been extracted to your hard drive. Press the command key and type ‘terminal’ to open a terminal window. At the command prompt, you should be able to run any workshop application by typing its name (e.g., try typing tophat). All of the workshop applications are installed in ~/wme_jan2013/local. Documentation and sample files from the various software installation packages can be found in ~/wme_jan2013/software. For more information about using the command line, please see our UNIX tutorial.
  8. At this point, all should be working well. Please begin to familiarize yourself with both the OS and the command line. Try connecting to the Internet using a wireless connection. You may need to install proprietary drivers for your wireless card, for which you may need to temporarily use a wired internet connection. Your regular Windows files can be found in /host. If you have any questions about your Ubuntu Linux installation, please ask an instructor.

Removal Instructions

If you wish to uninstall Linux from your computer, simply run the uninstaller in add/remove programs or use C:\ubuntu\Uninstall-Ubuntu.exe.