How to Run The PredictProtein Machine Image with VMware

From Rost Lab Open

VMWare Fusion is a virtual machine software product developed by VMware for Macintosh computers with Intel processors. It is a commercial product licensed by VMware inc.


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: File -> New -> Continue Without Disk
  4. Pick Use an existing virtual disk
  5. locate and pick your unarchivedmachine image (the extension should be vmdk)
  6. Name your virtual machine
  7. If you get this message: "This virtual disk was created with an older VMware product." click Convert
  8. Click Continue
  9. Set Operating System: Linux Version: Ubuntu-64bit
  10. Click Finish and name your new virtual image
  11. Give at least 2GB of RAM to your virtual machine from the Settings menu
  12. Your new virtual machine will now boot and and a bookmark will be created in the Virtual Machine Library for future boots
  13. If the message "The disk drive for /mnt/local-storage is not ready yet or not present" appears, press 's'.
  14. 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 VMWare Fusion 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 VMWare website