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How to Create a Virtual Machine

The software we will use for finishing is called Consed, written and maintained by David Gordon in Phil Green's lab at the University of Washington. It's freely available and widely used. Unfortunately, running it on Macs can be a little daunting (and it can't be run on Windows boxes at all), so we're going to try a workaround this semester. We will use a different program, called VirtualBox (version 4.0), to create a virtual Linux computer inside our Macs.

  1. Download the file GEP_live_CD_v2.iso from the Public > bio > BIO391 (Genomics) folder on pawn: (aka the P: drive) to your computer. It doesn't matter where you put it, but you'll want to be able to locate it later.
  2. Open the VirtualBox application (in the Applications folder).
  3. Click the New button in the upper left of the window.
  4. Click Continue in the lower right of the window.
  5. Name your machine; it doesn't matter what you call it.
  6. The Operating System and Version menus will probably change as you type in a name; whatever happens, make sure that they are Linux and Linux 2.6 after you've selected a name. Click Continue.
  7. Adjust the base memory size to 512 MB by using the slider or (easier) typing in the text box on the right side of the window. Click Continue.
  8. We want to create a virtual hard disk: leave the Boot Hard Disk checkbox checked and click Continue; click Continue again, leave the "Dynamically expanding storage" radio button selected and click Continue again. In the next window the name of your machine should appear in the Location window and the size will be 8.00 GB as a default; leave these as they are and click Continue again. Click Done in the next two windows. should appear after "SATA Port 0" in the Storage. section in the right half of the VirtualBox Manager window.
  9. Click on Storage.
  10. In the resulting window, click on the "Empty" entry under "IDE Controller" and then click on the small disk icon to the right of "IDE Secondary" in the right half of the window.
  11. Select "Choose a virtual CD/DVD disk file..." and navigate to the GEP_Live_CD_v2.iso file you downloaded earlier; this will link the virtual machine to the .iso file. If everything worked, GEP_Live_CD_v2.iso will now appear under "IDE Controller" where "Empty" was previously.
  12. Click "OK" to return to the VirtualBox Manager window; GEP_Live_CD_v2.iso should now appear under Storage in the right half of the window.
  13. To enable the use of a USB (a.k.a. thumbdrive or flashdrive) with the virtual machine, click on the "USB" heading in the panel on the right side of the VirtualBox Manager window. (You may need to scroll down to find it.)
  14. Important: leave the Enable USB 2.0 (EHCI) Controller box unchecked. Click on the small USB icon with the blue dot (on the right side of the window). If you want to change the name of the filter to something other than "New Filter 1," double-click on the name and go wild. When you're ready to proceed, click OK to return to the VirtualBox Manager window; you should now see that there is 1 active device filter.
  15. To start the virtual machine, double-click the entry in the top left of the window or click it once to select it (if it isn't already highlighted) and then click the rightward-pointing green arrow above it).
  16. You will get a lengthy warning about the "Auto capture keyboard" option; we'll discuss this in class, for now just click Okay.
  17. Your virtual machine should now start up automatically. (Hitting Enter at the first prompt will speed this process up.) After you exit, the machine will still exist so you don't need to go through all this every time you need to run Consed!
  18. To reduce the flakiness and unreliability of the cursor capture, go to the Machine menu (in the main menu bar when you''ve got the virtual machine open) and select "Disable Mouse Integration."
  19. When you've finished your session and quit Consed (after saving your work, of course!), log out of the virtual machine by either right-clicking on the virtual desktop and selecting Logout or by clicking on the Menu button in the bottom left of the virtual machine's desktop (in this iteration, it's a red bauble with a black spider on it) and selecting Logout.