VMware HOWTO

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VMWare Images

VMWare images containing GMOD software will let you try GMOD software without installing it on your local machine. Instead, the software runs inside a virtual machine on your computer. We will update these pre-configured virtual machine images over time, watch this page for more information. These virtual machines were created with RPM packages from http://biopackages.net. If you want to install this software directly on your computer please see the Biopackages HOWTO (we highly recommend using the CentOS 4 distribution with these packages).

Preliminaries

First, download either VMWare Fusion (beta) for the Mac or VMWare Workstation 6 for the Linux PC. Other versions of VMWare Workstation or VMWare Server should work for Windows and Linux but are currently untested.

Getting the VMWare Image

Once VMWare Workstation (or Fusion) is correctly installed you can download the VMWare images we have created that contain several GMOD tools pre-installed and configured. The images can be browsed and downloaded from the [Biopackages] server.

There are two images of interest that differ based on the software pre-installed:

  • A small VM ([centos4.i386.testing.04-23-07.v2.tar.gz]): includes GMODWeb, the Chado pre-loaded with Yeast data, and other software (AmiGO, Textpresso, BlastGraphic). No GUI is installed so the VM is small (~1GB).
  • A large VM ([centos4.i386.testing.06-18-07.tar.gz]): includes GMODWeb and Chado for both Human and Yeast, other GMOD software (AmiGO, Textpresso, BlastGraphic), and X11 with Gnome. A full desktop environment is preinstalled on this image and, as a result, the size is rather large (~7.3GB).

To install this VM download it and unzip/untar it to a directory of your choice.

Launching the VMWare Image

Now that you have the VMWare image downloaded and decompressed, launch VMWare. Either double-click on the Mac or in a terminal in Linux use the command:

vmware

Choose 'File->Open...' and navigate to the image directory you just decompressed. Locate the appropriate file and click 'Open'.

Next, click the 'Power On' button to boot up this virtual machine.

Using the VMWare Image

Now that the image is booted you may need to do some configuration depending on your environment. First, login as root (password is gmod). Next, make sure the network is setup correctly, it is currently configured to use DHCP. To change it issue the command:

system-config-network

and follow the directions.

PostgreSQL(database) and Apache (web server) should be running already. You can check by:

/etc/init.d/postgresql status
/etc/init.d/httpd status

If they are not start them:

/etc/init.d/postgresql start
/etc/init.d/httpd start

You can see what software is installed using the following RPM command:

rpm -qa | less

Using GMOD Apps

The Small Image

The image does not provide XWindows so you need to use Mozilla (or another web browser) on your host machine. Open http://VM_IP_ADDRESS in your browser and you should be redirected to the GMODWeb home page. You can try out GMODWeb, GBrowse, Textpresso, AmiGO, and BlastGraphic though this site.

The Large Image

When booted, this image will automatically log in as the gmod user (the password is gmod) and launch Mozilla. The root web page (http://localhost) describes the software installed and how to access it.

Support

Email either the main GMOD list [here] for application questions or the Biopackages list [here] for questions/problems with the VM itself.

Authors

Brian O'Connor