Plug-n-Play VariantDB using VirtualBox

Follow the steps below to get a private VariantDB instance up and running with minimal effort. It requires the Oracle Virtual Machine Manager 'VirtualBox'.

Install VirtualBox

Oracle VM VirtualBox is freely downloadable from their homepage. Note: The VariantDB-VM requires a 64bit host!

Download and activate VariantDB_VM

The following steps were tested on Windows 7 SP1 as a host with VirtualBox v4.2.12.

  1. Download the VariantDB OVA File (15gb, MD5: 6720e259d6b3470036ef933d29be0c40): Right-Click_Save-as to download
  2. Open VirtualBox Manager, select 'File'->'Import Appliance'. Browse to the downloaded variantdb.ova file.
  3. Right click the VM in the list and choose settings
  4. Set the number of RAM and CPUs to an appropriate value for your host. Note: to handle snpEff annotations, you need approximately 5-6gb of RAM.

Launch VariantDB

  1. Launch the Virtual Machine by right-clicking and selecting 'Start'
  2. Log in. The VM system user is 'administrator' with a password 'default'. Make sure to change this upon first login ! (execute 'passwd')
  3. Write down the network address: run `ifconfig` and write down the 'inet addr' for 'eth1'. It should be in a 192.168.x.x range.
  4. open credentials file : 'sudo nano /VariantDB/.Credentials/.credentials' (provide your password when prompted)
    1. Set <ADMINMAIL> to your email address.
    2. Set <DATAHOST> to the network address of the VM for IGVdata. This setting can be used to host BAM/VCF files on a remote server.
    3. Optional : enable FTP (FTP=1) and set the FTP_HOST value to the network address of the VM.
    4. Optional : USEMEMCACHED : if enabled, data are cached to improve performance. Be default, only localhost is used. More can be added as comma-seperated list
    5. Optional : Increase MYSQLTHREADS : allow multiple simultaneous connections to mysql to fetch filter & annotation data. Make sure to increase the number of CPUs in the VM appropriately.
    6. Optional : Enable HPC connection (USEHPC=1): if enabled, the VM will submit annotation scripts for new data to a high perforance cluster (torque-pbs). Make sure your HPC is configured to allow the VM to submit jobs
  5. Set the correct smtp server for outgoing emails in /etc/mail/ (Replace the entry).
  6. You can now close the VirtualBox Manager and minimize the VariantDB-VM Window. Recent VirtualBox systems can be started headless, in this case you can close the VM window completely.
  7. Note: The root password for the mysql database (accessible using phpmyadmin is also 'default'.

Initialize and update VariantDB

  1. In your browser, go to http://<variantdb-vm.ip.address/variantdb
  2. Fill in details for the administrator user of VariantDB
  3. Submit the form and wait for the confirmation. This can take a while, since VariantDB now performs various initialisation steps.
  4. Upon completion, you will be redirected to the home page. Login using the link in the top right corner
  5. To update your VariantDB version to the latest and greatest, go to "Settings => Platform updates". Take note that first load of this page can take a few minutes:
    1. First select all available options except the database revisions, and press submit
    2. Select 'Return to system updates'. Now update the database
    3. After confirmation that the database update was done, click the 'start update' link (if present) to update the annotation data sources

Load Demonstration Data

  1. Former DECIPHER employee, Manuel Corpas, has made exome data available for his family. A GATK-like analysis result is available at : The Main VariantDB WebSite
  2. First Download the data to your local computer, then upload using FTP to your VariantDB Instance:
    1. Log in on the VariantDB Website, go to 'New Data'
    2. Log-in details for your FTP server are listed there. If not, first provide your password to activate FTP access.
    3. Connect using an FTP client (eg FileZilla), and upload the BAM/VCF files to your root folder. Data in subdirectories can not be used by VariantDB
    4. Note: Make sure you adjust the size fo the ftp-data folder in the virtual machine to accomodate future data uploads. It is highly recommended to mount a network-share as the ftp-location.
  3. Go to 'New Data'. Provide the sample details, and select the correct files from the drop-down menus. Multiple samples can be added at once using the 'Load More Samples' button.
  4. Press 'Load Samples Into Database' to start the data import.
  5. Once the import is completed, you will recieve a notification by email.

VariantDB is now ready. Please note that it might take some time for the annotations to finish (indicated in the menu bar).