Install a BITS-training virtual-machine on your computer
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Download and install a prebuilt VirtualBox BITS Hands-On training virtual machine
Contents
2016-07-27, initial version 1.0
Some Hands-On Training session make use of Unix OS installed on BITS laptops. In order to allow motivated scientists repeat the session from the lab or at home, we provide virtual machines reproducing the OS and installed software seen during the sessions. Such machine can be deployed on a strong-enough personal computer and wil provide the environment and data recapitulating what was seen and done during the BITS training.
Some bioinformatic programs require a certain amount of memory and computing power (cpu) which are not available on the average laptop. For these harder to complete tasks, you will need to deploy the VM on a stronger desktop computer with a minimal performance of 8GB RAM and 4 cores (more is better).
Introduction
Download and install VirtualBox
Please refer to the Oracle pages (https://www.virtualbox.org/) for this part, they are very well illustrated and will guide you through this painless journey [1]. For help, please refer to the User Manual of the current VirtualBox release (PDF version)
Download the BITS OVA file containing the VM data
When VirtualBox is installed, you can start using it and create your first virtual machine. In order to recreate the BITS virtual computer, you will need one of the BITS OVA clone stored on our server. This large archive (30-60Gb) can be downloaded in about 1-3h with good internet bandwidth and should be placed on your computer hard-disk or on a mobile USB disk connected to it before import in VirtualBox.
The OVA file is not the final machine but an archive of it that needs to be extracted by VirtualBox (thereby temporarily doubling the required storage size. After import, the OVA file can safely be deleted or moved to some backup storage
A list of currently available VM-images can be found in Virtual-Machines_supporting_Hands-on_Sessions
Create a virtual machine from the BITS OVA file
VirtualBox reads the OVA file and creates the virtual disks and environment necessary to reproduce a functional virtual computer. In order to import the OVA data, please follow the tutorial presented here. The initial settings for the VM are using 4GB of RAM and 2 cores.
During import, you can adapt some of the system parameters in order to match them to your own host computer. Please try to dedicate as much resources as possible to the VM in order to make possible heavier computing tasks. A good performance should be obtained with at least 4cpu and at least 16GB RAM.
Initial VM parameters
Start the virtual machine and log into the BITS account
Taking the NGS-Variant training as example.
After the machine is started it should present you the login page. You should use the BITS user as during the training session with associated password training.
Please note that this user has root access, meaning he has authority to do everything on the virtual machine, including adding other tools or destroying its content
You will find the training data in the second hard-disk called Variant_DATA as well as a NGS-Variant-Analysis-training-2016 folder ready to start with in the BITS home folder. Open a terminal session, then type
cd $BASE ls -lah
Become fluent in Biocomputing
You are now at the place where all scripts should be run to reproduce the training, for further info, please refer to the Hand-On training wiki pages. Please use and share this machine and let us know what may not work optimally.
Happy Biocomputing!
References:
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