Wójcikowski MaciejJust another blog about cheminformatics and bioinformatics

myChEMBL running on KVM

Recently ChEMBL team released a revised version on myChEMBL (#18) virtual machine, which is standalone image for VirtualBox. myChEMBL allows to deploy your private ChEMBL, although not fully featured, but still very useful.  Actually the new release supports installing VM straight from the Vagrant Cloud, which is “just two commands”.  But… That’s the case if you have Vagrant set up, or at least Virtual Box, which might not be straightforward. Here, I give you few tips how to run the myChEMBL on generic Linux hypervisor – KVM. It’s really easy if you know your way around VMs in general, but for those not that familiar with KVM this steps should save the day.

  1. Download myChEMBL image [link], just the largest disk image with .vmdk extension
    • wget ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/releases/myChEMBL-18_0/myChEMBL-18_0-disk1.vmdk

  2. Convert the image to qcow2. Although KVM supports vmdk, myChEMBL image doesn’t work.
    • qemu-img convert -c myChEMBL-18_0-disk1.vmdk -O qcow2 myChEMBL-18_0-disk1.qcow2

    • note the -c option which enables compression in qcow2 image, without it the VM would take over 18GB of space
  3. Create VM (I use Virt-Manger) and set qcow2 image as primary storage.
  4. Startup VM
  5. Finished! When the VM is booted (it might take a while, since some “hardware” has changed), you can access it using web browser using VM’s IP.