How to Run The PredictProtein Machine Image with VirtualBox

From Rost Lab Open

VirtualBox Fusion is a powerful x86 and AMD64/Intel64 virtualization product for enterprise as well as home use. it is freely available as Open Source Software under the terms of the GNU General Public License (GPL) version 2.


This procedure assumes that:

  • 1.5G memory is available for the virtual machine.

Preparing the PredictProtein Machine Image for First Use

  1. Download PredictProtein Machine Image to your local drive. You will need the Bio-Linux-based 'VMWARE/VMDK' format version.
    • Choose the Debian-based version in case you do not need a graphical user interface. This image is only half the size of the Bio-Linux-based image.
  2. Download a database image to your local drive. We recommend the 'raw' format version.
  3. Create New Virtual Machine: Machine -> New
  4. Name your virtual machine as 'PredictProtein'
  5. Choose Linux and Debian as operation system
  6. Locate and select the VMware .vmdk file as your boot disk
  7. Give at least 2GB of RAM to your virtual machine
  8. Click 'Finish'
  9. Boot your new virtual machine.
  10. If the message "The disk drive for /mnt/local-storage is not ready yet or not present" appears, press 's'.
  11. Open a terminal and enter:
    1. sudo mkfs.ext4 -F -m 0 -L local-storage /dev/sdb
    2. sudo mount -a
    3. sudo mkdir /mnt/local-storage/rostlab-data && cd /mnt/local-storage/rostlab-data
    4. sudo mount -a
    5. sudo mount /mnt/rostlab-data
    6. sudo tar -xvJf /mnt/rostlab-data/rostlab-data.txz
    7. sudo umount /mnt/rostlab-data && cd

Using the PredictProtein Machine Image

  1. Start VirtualBox and run the 'PredictProtein' image.
  2. Open a terminal and run man ppmi to get started. You will find usage examples in the manual pages referenced there, e.g.:
    • man predictprotein
    • man snapfun

More information is available on the Virtualbox website