Galaxy VM

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Revision as of 14:34, 10 February 2011 by David.van.enckevort (Talk | contribs)

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In collaboration with the people running the NBIC Galaxy Server, the BioAssist Engineering Team has made scripts that can extract a Galaxy Virtual Machine that has all the NBIC galaxy tools available. Users can download the virtual machine and run it on their local hardware.

Our goals are:

  • Easy installation and configuration of a local Galaxy server
  • Run a local Galaxy so that you don't need to transfer 10's of GBs of data via Internet and worry about data security and privacy
  • We will shared all NGS/Proteomics pipelines developed by NBIC developers via the NBIC Galaxy VM

Minimal system requirements

The virtual machine can run with as little as 1GB of RAM assigned to it. It has a 100GB virtual harddisk and it requires a single network interface that is connected to your network (no NAT or local machine network). The actual amount of memory required depends on the number of users and the kind of jobs you run. When working with large datasets it can not hurt to assign an ample amount of memory.


  • Step 1: Install VM software

To run the VM you will need a version of the VMware hypervisor, for evaluation or small deployments the free versions (VMware Player, VMware Server or VMware vSphere Hypervisor (ESXi)) can be used, for a production environment it is recommended to run on VMware vSphere. Other hypervisors are currently not directly supported by NBIC, but if you disable the VMware Tools in the virtual machine you should be able to run it in KVM, VirtualBox, Xen or VirtualPC as well. We are always interested to hear about your experiences with other hypervisors.

  • Step 2: Download NBIC Galaxy VM

The latest virtual machine image is available at (A torrent file is available at BioTorrents). It is a VMware virtual machine image.

  • Step 3: Load Galaxy VM
    • The Virtual Machine image is based on CentOS 5.5 64-bit (RedHat Enterprise Linux compatible). You should create a new virtual machine for this distribution or the closest match. In the virtual machine you need to configure memory, networking and configure the virtual disk to point to the galaxy (.vmdk) disk image.
    • The image has an admin login account with username admin and password install123 and supports sudo to execute administrative tasks. Please take the hint and change the password of this account before making your VM available on the network.
    • If the virtual machine is configured to request an IP address by DHCP. If DHCP is available, but it fails to bring up the network interface there is a mismatch between the MAC address of the virtual machine and the MAC address configered in the image. You can resolve this by editing the file /etc/sysconfig/network-scripts/ifcfg-eth0 and update the line HWADDR with the correct MAC address. If DHCP is not available you need to reconfigure the network with command sudo system-config-network-tui for your network, please consult with your network administrator for the correct network settings. On reboot the machine should display the URL to access galaxy on the console.
  • Step 4: Access Galaxy VM

To access the Galaxy you should go to http://<ip-address>/galaxy/ the / at the end of the URL is currently required (will be fixed in a later release of the VM)

  • We strongly suggest that you make a snapshot or a copy of your virtual machine before going into production. This allows you to reset it to a clean state easily if required.


  • Why I receive errors during the download of the NBIC Galaxy VM?

First, check to see whether your Internet connection works or not. It is always nice to use a download manager. Make sure you have a 64bit system as 32bit system can't support a file larger than 2GBs.

  • What should I do if I want more disk space for the VM?

Currently the virtual machine has 100GB local storage. If necessary you can extend the size of the image, but this is not trivial. If disk space is a big issue you can also relocate the /nbic directory to a network shared disk. Consult with your system administrators to see if this is possible and how to set this up. Fast network access is recommended if you choose this option.

The virtual machine does not run any cleanup jobs yet, to prevent running out of diskspace you should configure the cleanup jobs. See the galaxy documentation on how to setup these jobs.


Please contact for any question you have regarding the Galaxy VM.