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QIIME Virtual Box: Before you start

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Greg Caporaso edited this page May 22, 2015 · 10 revisions

Copy/paste in the Virtual Box

To copy and paste to and from all applications except the terminal, use control-c and control-v, respectively. To copy and paste to and from the terminal, use control-shift-c and control-shift-v, respectively. Note however that you will need to install the guest additions BEFORE this works. The steps for installing the guest additions are described in this document. You can also copy and paste via the 'Edit' menu before or after installing the guest additions.

Installing Guest Additions

Before getting started with QIIME, you should install the VirtualBox guest additions. The guest additions are a set of applications that will be installed in the virtual machine to add convenient functionality, including enabling a larger display window.

To install the guest additions:

  1. Log into the Linux virtual machine, if you haven't. Remember the password is qiime.

  2. Go to the VirtualBox menu and select "Devices" -> "Install Guest Additions CD Image". This brings up The Virtual Media Manager, described in Section 5.3. If your mouse is "trapped" in the virtual machine you can release the mouse pointer using either the left Command-key (Mac) or the right Control-key (Windows).

  3. If a new pop up window opens, just close it.

  4. Open a terminal window in the virtual machine by clicking on the black icon with a > in the side menu bar of the virtual machine.

  5. Run the installation in the terminal by typing: sudo /media/VBOXADDITIONS_[your_version]/VBoxLinuxAdditions.run and then hitting "Enter". When prompted, enter qiime. Note that the directory name VBOXADDITIONS_[your_version] will depend on the version of your VirtualBox (you can type sudo /media/VBOXADDITIONS_ and then hit the tab key to autocomplete). Alternatively, you can determine the directory name by running ls /media and finding it in the resulting list of file and directory names.

  6. When that command is finished running (i.e., you get a command prompt back), restart the virtual machine by clicking the power button to the right of the username (Qiime User) in the upper right corner of the virtual machine window and then selecting Shut Down.... Click Restart when prompted.

After the Virtual Box restarts, you're ready to start using QIIME! Please visit www.qiime.org for documentation, tutorials, and other resources. For getting help with QIIME, please visit help.qiime.org.

Fixing internet access in the Virtual Box

If your virtual machine does not have Internet access, follow these steps:

  1. Open a terminal and run the following command:
sudo lshw -c network

This should show you the network card(s) available to your virtual machine. Look for their "logical name" and write them down.

  1. Run the following command to open a file for editing:
sudo gedit /etc/network/interfaces
  1. For each network card available, add entries to this file that look like:
auto <logical_name>
iface <logical_name> inet dhcp

For each entry, be sure to replace <logical_name> with the logical name of the network card from step 1.

  1. Run the following command:
sudo /etc/init.d/networking restart

You may need to restart the virtual machine again. You will only need to do this once.

Transferring files to and from the Virtual Box

IMPORTANT: You need to install the guest additions BEFORE this will work (see the instructions above).

To analyze your data with the QIIME Virtual Box you will need to have access to your files inside of this virtual machine. There are several ways to accomplish this, including:

  1. E-mail the data to yourself, if size permits, and check your email using a web browser (e.g., Firefox or Google Chrome) within the virtual box.

  2. Create a shared folder between your real machine (the host) and the virtual machine (the guest):

  • At the bottom of the virtual machine screen there are some icons. On Mac OS X: Click once on the blue/grey folder. On Windows: Right-click on the blue/grey folder.

  • Select "Shared Folders Settings..."

  • A new window will open. Select the blue/grey folder icon with a green plus sign on the right of the new screen.

  • A new window will open. On the "Folder Path" option select the down arrow and click on the "Other..." option.

  • A new window will open. Select the folder that you want to share with your virtual machine. Click OK.

  • Change the "Folder Name" option to Shared_Folder, select the "Make Permanent" option and make sure that the "Read-only" option is not selected. Click OK.

  • Click OK.

  • Open a terminal on your virtual machine and run the following command:

    sudo mount -a

If you do this every time you restart your machine you will have the connection to your real machine through the Shared_Folder on your virtual machine desktop.

  1. Post the data on an external server and retrieve it using wget, scp, sftp, etc.

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