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.
- Download the VariantDB OVA File (15gb, MD5: 6720e259d6b3470036ef933d29be0c40): Right-Click_Save-as to download
- Open VirtualBox Manager, select 'File'->'Import Appliance'. Browse to the downloaded variantdb.ova file.
- Right click the VM in the list and choose settings
- 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
- Launch the Virtual Machine by right-clicking and selecting 'Start'
- Log in. The VM system user is 'administrator' with a password 'default'. Make sure to change this upon first login ! (execute 'passwd')
- 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.
- open credentials file : 'sudo nano /VariantDB/.Credentials/.credentials' (provide your password when prompted)
- Set <ADMINMAIL> to your email address.
- 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.
- Optional : enable FTP (FTP=1) and set the FTP_HOST value to the network address of the VM.
- Optional : USEMEMCACHED : if enabled, data are cached to improve performance. Be default, only localhost is used. More can be added as comma-seperated list
- 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.
- 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
- Set the correct smtp server for outgoing emails in /etc/mail/sendmail.cf (Replace the smtp.ua.ac.be entry).
- 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.
- Note: The root password for the mysql database (accessible using phpmyadmin is also 'default'.
Initialize and update VariantDB
- In your browser, go to http://<variantdb-vm.ip.address/variantdb
- Fill in details for the administrator user of VariantDB
- Submit the form and wait for the confirmation. This can take a while, since VariantDB now performs various initialisation steps.
- Upon completion, you will be redirected to the home page. Login using the link in the top right corner
- 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:
- First select all available options except the database revisions, and press submit
- Select 'Return to system updates'. Now update the database
- After confirmation that the database update was done, click the 'start update' link (if present) to update the annotation data sources
Load Demonstration Data
- 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
- First Download the data to your local computer, then upload using FTP to your VariantDB Instance:
- Log in on the VariantDB Website, go to 'New Data'
- Log-in details for your FTP server are listed there. If not, first provide your password to activate FTP access.
- 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
- 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.
- 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.
- Press 'Load Samples Into Database' to start the data import.
- 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).