Difference between revisions of "VMware HOWTO"

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[[File:VmwareLogoSmall.jpg|right|link=http://vmware.com|VMware]]
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[http://vmware.com VMware] images containing GMOD software let you try GMOD software without installing it on your local machine.  Instead, the software runs inside a virtual machine on your computer.
  
=VMWare Images=
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VMware images are used in several places in GMOD:
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* The [[Community Annotation System]] is packaged as a VMware image.
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* Many GMOD [[:Category:Tutorials|tutorials]] use VMware images as starting points.
  
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 | Biopackages HOWTO]] (we highly recommend using the CentOS 4 distribution with these packages).
 
  
=Preliminaries=
 
  
First, download either [http://www.vmware.com/products/beta/fusion/ VMWare Fusion] (beta) for the Mac or [http://www.vmware.com/products/ws/ 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.
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= VMware Players =
  
=Getting the VMWare Image=
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{{VMwareOptions}}
  
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 [[http://biopackages.net/vmware_images Biopackages]] server.
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= Getting the VMware Image =
  
The most recent VMWare image (centos4.i386.testing.04-23-07.v2.tar.gz) includes GMODWeb and Chado pre-loaded with Yeast data.
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Anything that uses a VMware image will have a link to the image on its wiki page.  Once you have the VMware player software installed (see [[#VMware Players|VMware Players]]), download the image on to your system. You will need to unpack the downloaded file (usually you'll need to unzip and/or untar it) before loading it into your VMware player software (see [[#VMware Players|VMware Players]]). Most images have been compressed with tar and/or gzip.
  
To install this VM download it and unzip/untar it.
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= Starting the VMware Image =
  
=Launching the VMWare Image=
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Details on starting the VMware image vary from platform to platform.  See the documentation for your VMware player for how to do start an image on your system.
  
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:
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If you are running a player from VMware (VMware Player or Fusion), the software will ask you if you moved or copied the image.
  
vmware
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<div class="emphasisbox" style="text-align: center"> <div style="font-size: 160%">You Moved It!</div>
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Yes you did.
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</div>
  
Choose 'File->Open...' and navigate to the image directory you just decompressed.  Locate the appropriate file and click 'Open'.
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If you say you copied it, you will have to do additional network configuration once it is up and running.
  
Next, click the 'Power On' button to boot up this virtual machine.
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= Using the VMWare Image =
  
=Using the VMWare Image=
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After starting up the VMware image (which will take several seconds), you will be greeted with an attractive text-based terminal.  Login using the username and password for the system (which should be listed on the wiki page you downloaded the image from.
  
Now that the image is booted you may need to do some configuration depending on your environment. First, login as root (password is gmodchado)Next, make sure the network is setup correctly, it is currently configured to use DHCP.  To change it issue the command:
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At this point, you have a few options for how to use itIf you would like to ssh in to the server (which I suggest as a good idea: copy and pasting commands will be easier and you will be able to use an environment you are used to), then you will need the server's ip address.  To get it, at the command prompt, type:
  
system-config-network
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  ifconfig
  
and follow the directions.
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which will give you output like this:
  
PostgreSQL(database) and Apache (web server) should be running already.  You can check by:
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[[Image:Ifconfig_output.jpg]]
  
/etc/init.d/postgresql status
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See that "inet addr:172.16.244.128"? Those four numbers are the IP address. You can now (from you host operating system) ssh into the machine by typing
  /etc/init.d/httpd status
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If they are not start them:
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  ssh gmod@172.16.244.128
  
/etc/init.d/postgresql start
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You can also go to the web server running on this server by going to http://172.16.244.128 (for example). If you are on Windows and would like to do this, you can get [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html putty], which is a free ssh client for windows.
/etc/init.d/httpd start
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You can see what software is installed using the following RPM command:
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= Fluxbox =
  
rpm -qa | less
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The images from most 2009 [[:Category:Tutorials|Tutorial]] pages include a basic ''{{GlossaryLink|GUI|graphical user interface}}'' called ''[http://fluxbox.org/ Fluxbox]''.  Fluxbox is a minimal GUI.
  
=Viewing GMODWeb=
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If you want to use a graphical user interface on these images, using a browser and terminal inside the VMware image, you can start X11/Fluxbox by typing:
  
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.
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  startx
  
=Authors=
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on the command line, and the GUI will start up.  After it starts up, you can right click (or control-click) to get a menu that will start applications like Firefox and terminal.
 
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[[User:Boconnor|Brian O'Connor]]
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[[Category:HOWTO]]
 
[[Category:HOWTO]]

Latest revision as of 18:43, 17 September 2012

VMware

VMware images containing GMOD software let you try GMOD software without installing it on your local machine. Instead, the software runs inside a virtual machine on your computer.

VMware images are used in several places in GMOD:


VMware Players

Which software to use to run VMware images depends on the operating system you will run the image under. (It does not depend on the operating system inside the VMware image.)

VMware on Windows and Linux
Windoze
Linux

A free VMware player is available for Microsoft Windows and Linux operating systems from VMware. You will need to register to download it. There are multiple versions. Be sure to download a version that can run on your laptop.


VMware on Mac OS X
Apple

Participants can also bring newer Macs with Intel processors. The Intel processor is a requirement for all the packages discussed below. There is no free VMware player that runs directly under Mac OS X. However, there are several other options, all of which require an Intel Mac:


VMware Fusion
Fusion

VMware Fusion ($80/corporate, $40/Academic) allows you to run VMware images (as well as Windows and Linux) under Mac OS. We recommend this option for Mac users. There is a fully functional, 30 day free trial version of VMware Fusion available for download.


VirtualBox
VirtualBox

VirtualBox is free and open source, and runs on Intel Macs (and Windows, Linux and Solaris too). It claims to be capable of running VMware images, but we have not tested this with our images.

Getting the VMware Image

Anything that uses a VMware image will have a link to the image on its wiki page. Once you have the VMware player software installed (see VMware Players), download the image on to your system. You will need to unpack the downloaded file (usually you'll need to unzip and/or untar it) before loading it into your VMware player software (see VMware Players). Most images have been compressed with tar and/or gzip.

Starting the VMware Image

Details on starting the VMware image vary from platform to platform. See the documentation for your VMware player for how to do start an image on your system.

If you are running a player from VMware (VMware Player or Fusion), the software will ask you if you moved or copied the image.

You Moved It!

Yes you did.

If you say you copied it, you will have to do additional network configuration once it is up and running.

Using the VMWare Image

After starting up the VMware image (which will take several seconds), you will be greeted with an attractive text-based terminal. Login using the username and password for the system (which should be listed on the wiki page you downloaded the image from.

At this point, you have a few options for how to use it. If you would like to ssh in to the server (which I suggest as a good idea: copy and pasting commands will be easier and you will be able to use an environment you are used to), then you will need the server's ip address. To get it, at the command prompt, type:

 ifconfig

which will give you output like this:

Ifconfig output.jpg

See that "inet addr:172.16.244.128"? Those four numbers are the IP address. You can now (from you host operating system) ssh into the machine by typing

 ssh gmod@172.16.244.128

You can also go to the web server running on this server by going to http://172.16.244.128 (for example). If you are on Windows and would like to do this, you can get putty, which is a free ssh client for windows.

Fluxbox

The images from most 2009 Tutorial pages include a basic graphical user interface called Fluxbox. Fluxbox is a minimal GUI.

If you want to use a graphical user interface on these images, using a browser and terminal inside the VMware image, you can start X11/Fluxbox by typing:

 startx

on the command line, and the GUI will start up. After it starts up, you can right click (or control-click) to get a menu that will start applications like Firefox and terminal.