How to Run the PredictProtein Machine Image with libvirt

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libvirt is a toolkit to interact with the virtualization capabilities of recent versions of Linux (and other OSes). libvirt is free software available under the GNU Lesser General Public License.

Prerequisites

This procedure assumes that:

  • You carry the steps out as 'root'.
  • A 'dir'-type pool called 'default' is available at /var/lib/libvirt/images.
  • Pool 'default' has at least 32G free space.
  • 1.5G memory is available for the virtual machine.

Preparing the PredictProtein Machine Image for First Use

  1. Download PredictProtein Machine Image to 'default' pool. We recommend the Bio-Linux-based 'raw' 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 'default' pool. We recommend the 'raw' format version.
  3. Create a new volume of at least 20G:
    virsh vol-create-as default local-storage 20G
  4. Define a new domain 'predictprotein':
    1. Download File:Libvirt-pp-domain.xml to /tmp/Libvirt-pp-domain.xml.
    2. Edit the XML file if your pool is not at /var/lib/libvirt/images or the images you downloaded are not 'raw' format.
    3. Edit the XML file if you want to give more memory to the virtual machine.
    4. Run virsh define /tmp/Libvirt-pp-domain.xml.
  5. Start virt-manager and run the 'predictprotein' domain.
  6. If the message "The disk drive for /mnt/local-storage is not ready yet or not present" appears, press 's'.
  7. 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
    8. It is not required, but you can now use virt-manager to remove the rostlab-data volume 'SCSI Disk 3' from the domain.

Using the PredictProtein Machine Image

  1. Start virt-manager and run the 'predictprotein' domain.
  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
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