Virtual Machines
Contents
Overview
"Virtual Machines" (or VMX) are self-contained packages of everything you need to use WormBase locally. To keep downloads small, we've split virtual machines into two components. First, you will need the primary virtual machine, which contains the WormBase software, within a Linux operating system.
Once you have the software, you can download which datasets you are interested in. We supply these as "virtual disks" -- consider these removable disks exactly like you might have sitting next to your laptop. Download only what you need, such as C. elegans predictions, WormMart, etc.
Virtual machines can be "played" on Mac, Windows, and Linux platforms using the free VMPlayer (Linux, Windows) or the (non-free how do you like them apples?) VMWare Fusion Player (Mac) available from VMWare.
Running a virtual machine of WormBase is incredibly easy.
- Download the VMPlayer from VMWare
- Download a WormBase virtual machine
- Select the datasets you'd like to use and download them
- Open the virtual machine using VMPlayer or VMFusion
- Log in
- A browser launches automatically and takes you to your copy of WormBase!
System Requirements
- Mac (with Intel chips), Windows, or Linux computer
- Virtualization Player (free): VMPlayer (Linux/Windows); (non-free) VMWare Fusion (Mac)
- 1 GB free memory (2GB recommended)
- 30 - 50 GB free disk space
- A BitTorrent client such as Azureus
Available Virtual Machines
WormBase virtual machines are preconfigured for use on the desktop. This means that they are intended to be run and used on the same local machine. If you would like to run the virtual machine as a server you will need to make some small changes to the configuration. See the section "Running a WormBase Virtual Machine as a server" for additional details.
NOTES:
1. Due to their size and limited distribution, torrents of older releases may not be available. If you would like an older release, please send a request to Todd Harris (harris@cshl.edu).
2. We have been having trouble with BitTorrent seeds timing out. Until this problem is resolved, please fetch the virtual machine using HTTP (and a client like wget or curl so that you can resume a download if it fails.)
| Release | Date | Size | via .torrent | via HTTP | md5 |
|---|---|---|---|---|---|
| WormBase WS175 | 27 May 2007 | 7.7 GB | Available by request |
md5 (e6615802e94133f8706d9177a71a521f) | |
| WormBase WS174 | 06 May 2007 | 9.0 GB | Available by request |
md5 (b6d74790c486167eaa1e7083e53921d8) | |
| WormBase WS173 | 15 Apr 2007 | 8.2 GB | Available by request |
md5 (7b3d6569a09a6e6d2ab9d6674c1d3af8) | |
| WormBase WS172 | 25 Mar 2007 | 7.9 GB | Available by request |
md5 (531f2d1f1ee85d5d05a75e928494dd1a) | |
| WormBase WS171 | 04 Mar 2007 | 8.5 GB | Available by request |
md5 (bf073383dc74e7292fef0f580c35b54a) | |
| WormBase WS170 | 09 Feb 2007 | 6.6 GB | Available by request |
md5 (fa64d32a5dc3f9322a7a1db95aa0fe8b) | |
| WormBase WS160 | 31 Jul 2006 | 7.1 GB | Available by request |
md5 (4aab931717dd384c05ef6bcae5e90ff9) | |
| WormBase WS150 | 30 Nov 2005 | 6.2 GB | Available by request |
md5 (f30131fc6d2f5418e55c7c6baa847e6f) | |
| WormBase WS140 | 26 Mar 2005 | 4.9 GB | Available by request |
md5 (262b4907d388107b24b1eded861fe214) | |
| WormBase WS130 | 16 Aug 2004 | 4.0 GB | Available by request |
md5 (7644914a7ab10b8100b4cf5c54d177f2) | |
| WormBase WS120 | 07 Mar 2004 | 3.5 GB | Available by request |
md5 (1727f2ac001e7d0f33502d99ab6606c2) | |
| WormBase WS110 | 01 Oct 2003 | 3.6 GB | Available by request |
md5 (d01a4da5d751393f9b507fdaf2727ca5) | |
| WormBase WS100 | 10 May 2003 | 3.3 GB | Available by request |
md5 (caa7290271451e38ff6600b517f49e18) |
Download Instructions
Downloading via the command line client curl
1. Open a terminal window
2. Type the following commands
curl -O http://www.wormbase.org/vmx/WS150.vmx.tgz curl -O http://www.wormbase.org/vmx/WS150.vmx.tgz.md5 md5sum --check WS150.vmx.tgz
Downloading via BitTorrent
Because of their size, virtual machines are available on the BitTorrent network. BitTorrent is a distributed peer-to-peer file sharing protocol that facilitates the download of large files. It does this by splitting files into many pieces. As each piece is fetched, its made available for others to download, doubling the number of copies of that segment. Instead of downloading one monolithic file from a single server, that same file can be downloaded piecemeal from potentially many servers.
1. Download and install a BitTorrent client
In order to fetch the WormBase BitTorrent files, you need either the official BitTorrent client or Azureus.
I recommend Azureus. Alternatively, you might try the official Bittorrent client.
2. Download one of the small BitTorrent files for a desired release
3. Open the .torrent file in the BitTorrent client.
NOTE: When you have finished downloading, please keep your BitTorrent client open in order to help share the load of distributing WormBase releases.
Fetching new releases automatically
WormBase creates new virtual machines for every release of the database. Your computer can fetch these for you automatically using the following script.
forthcoming - this script is still under development
Unpacking a downloaded torrent
Once you've completely downloaded one of the releases, unpack it using tar/gzip. I've had bad luck extracting the file with things like the BomArchiveHelper.
prompt> ls -rw-rw-r-- 1 todd todd 8.5G Mar 8 13:06 wormbase-WS171.2007.03.04.tgz prompt> tar xzf wormbase-WS171.2007.03.04.tgz
Note: Do make sure that you have 30-50 GB of disk space free prior to unpacking!
Using a WormBase Virtual Machine
Starting the Virtual Machine
Launch your Virtual Player / VM Fusion. From the File menu, select "Open". Navigate to the unpacked directory of the WormBase Virtual Machine. Open it. Inside, you will find a file ending with the suffix ".vmx". Select it, then select OK. The Virtual Machine will start to boot up.
Logging in
Log in as
User: wormbase Pass: wormbase
After logging in, a browser window will appear taking you directly to your local copy of WormBase.
Advanced uses
Each WormBase Virtual Machine contains the entirety of WormBase. This makes it a great tool for tasks like data mining. You can also use individual components of WormBase to best suit your needs.
Xace - the graphical interface to AceDB
/usr/local/acedb/bin/xace /usr/local/acedb/elegans
Tace - the text interface to AceDB
/usr/local/acedb/bin/tace /usr/local/acedb/elegans
AcePerl - Perl API to AceDB
Mine the underlying AceDB database programmatically using AcePerl.
Bio::DB::GFF - Perl API to genomic annotations
Each virtual machine contains multiple mysql databases of genomic annotations, including (as of WS170, 2/2007), C. elegans, C. briggsae, and C. remanei. You can use the Bio::DB::GFF API -- part of BioPerl -- to easily mine these sequence annotations.
Running a WormBase Virtual Machine as a server
Each WormBase Virtual Machine contains everything that you need to run it as a standalone server. In server mode, you can install a single copy of WormBase locally and make it available to others in your lab or organization, or even establish your own local mirror of WormBase accessible to all.
To do this, you will need to modify a few settings of the virtual machine. The main consideration for running a virtual machine as a server is how to manage networking. Described below are the two most suitable approaches. Bridged networking is the easiest and requires no additional components.
Using a VM with bridged networking
When run in bridged networking mode, the VMX shares the host OSs internet connection. This allows the guest OS to run with its own domain name and IP address.
1. Acquire a static IP and suitable domain name for your virtual machine
2. When launching the virtual machine, for networking, select "Bridged".
3. Configure network settings with your IP, domain name, and subnet mask.
In this example, the guest OS IP is 143.48.220.208. This should be changed to whatever your assigned IP address is.
ifconfig eth0:0 143.48.220.208 netmask 255.255.255.0 broadcast 143.48.220.255 route add -host 143.48.220.208 dev eth0
You can also do this from the GUI if you prefer, under System Settings -> Network. Double click on the network adaptor.
Address: Your assigned IP address Subnet mask: 255.255.255.0 Default gateway: 143.48.220.254 Broadcast host: 143.48.220.255 (not explicitly set in the GUI)
4. Reset the MAC ID of the guest
System Tools > Network
Double click on the network adaptor and select the "Hardware" tab. Click on "Probe", then "OK"
5. Add the following lines to /etc/resolve.conf for DNS. For our example, these are:
search cshl.edu nameserver 143.48.1.1 nameserver 143.48.1.20
6. Set the hostname
This can be done either in the GUI under the Network panel, or using the following command line terms.
If you have a static IP address, then /etc/hosts is configured as follows:
127.0.0.1 localhost.localdomain localhost 143.488.220.44 mybox.mydomain.com mybox
After updating the /etc/hosts file correctly, the "hostname" command should be run as follows to set your hostname:
hostname mybox.mydomain.com
7. Edit /usr/local/wormbase/conf/localdefs.pm and httpd.conf with the appropriate hostname as necessary.
8. Place the VM into console mode:
Comment out the runlevel 5 directive and uncomment the id3 runlevel directive in /etc/inittab:
$ sudo perl -p -i -e 's/id:5:initdefault:/#id:5:initdefault:/' /etc/inittab $ sudo perl -p -i -e 's/#id:3:initdefault:/id:5:initdefault:/' /etc/inittab
9. Shutdown the virtual machine and copy it as a backup
I append "server" to the name to indicate that it is configured as a server
tar czf wormbase-WS100.2003.05.13-server.tgz wormbase-WS100.2003.05.13
10. Restart the Virtual Machine. You should be good to go!
Using a VM with NAT addressing
By default, WormBase virtual machines use NAT networking. If you would like to use a server in NAT mode, you will need to configure an upstream proxy server (Apache or Squid, for example) to access the virtual machine remotely.
Troubleshooting
Resetting the MAC address
MAC addresses are set automically in virtual machines based on the host OS name and the path to the .vmx file on the host OS. If you move the virtual machine, the MAC address will be incorrect.
When booted into graphical mode:
System Tools > Network
Double click on the network adaptor and select the "Hardware" tab. Click on "Probe", then "OK".
