GenoVault

GenoVault "A Cloud Based Genomics Repository"

GenoVault is a private cloud-based central repository for storage and retrieval of genomics data generated in various research labs in various organizations. The solution is delivered in the form of a software suite called “GenoVault”, that enables quick archival and retrieval of data along with analytical support. GenoVault is based on OpenStack cloud. It exploits and utilize the full advantage of Cloud Computing viz, distributed computing and object storage. Users can upload the genomics sequence data onto the Cloud using Web or JavaFX based standalone interface along with metadata which is stored in the form of distributed objects on the cloud. This feature enables swift and efficient retrieval and storage of the genomics data. This centralized repository would be of enormous importance for genomics research labs.

Key Features:

• Web-based user-friendly interface
• Standalone Desktop Client
• Capable of transferring files of sizes > 50GB
• Every user has their own area for upload or download of data
• Data is stored into the Cloud as Object
• The Object will be stored in a distributed manner across swift nodes
• Distribruted storage enables efficient retrieval of the genomics data
• Solution is capable of scaling vertically and horizontally

Sample Input Data

Sample Input data is provided here.
Link for the sample input data download Click here

Usage

Using the deployed WAR and Jar file, the tool can be as web client over the internet and executed on any stand-alone desktop machine. Upload the genomics file over the Cloud with n number of the object's nodes.Following is the way to install and execute it.

Installation

Pre-requisites

---

• Must:

  • Java 1.8 or above Click here

  • MySQL 5 or above Click here

  • OpenStack Cloud Setup Click here

  • Swift based Object Storage Setup Click here

  • Wildfly 10.x server Click here

Application Structure for openstack-based GenoVault

---

								-------------------------
								|			|	
							________|Object Storage Node 1	|	
						      /		|			|	
						     /		-------------------------
						    /	
						   /
						  /				-------------------------
=================		=================/				|			|
| Application 	|		|		|  				|Object Storage Node 2	|
|  Server	|---------------|Controller Node|_______________________________|			|
|		|		| 		|				-------------------------
=================		=================\
						  \
						   \ 		-------------------------
						    \		|			|	
						     ___________|Object Storage Node 3 	|	
								|			|	
								-------------------------

Application Server: This is the node where the GenoVault Portal is deployed. 
Controller Node: This is the node where the Cloud Entry point.
Object Storage Nodes : These are nodes where the container will be created.
Note : All the nodes, except Application Server, are a part of OpenStack Cloud.

Server Side

JDK
Install Java 1.8 or above Click here

MySQL

    Install MySQL Server 5.6.33 or above
        $ sudo apt update
        $ sudo apt install mysql-server
        $ sudo mysql_secure_installation

Download GenoVault Database MySql dump

Link for the mysql data Click here

Import the default database

     $ mysql -u root -p
        mysql> CREATE DATABASE genovaultdb;
        $ mysql -u root -p < genovault.sql;
    Set environment variables.
        $ mkdir -p $HOME/genovault/upload
        $ mkdir -p $HOME/genovault/download
        $ cat >> .bashrc <<EOF 
                export GENOVAULT=$HOME/genovault

Web Based Client:

Download Widfly 10.x server

Wildfly 10.x server Click here

Extract

	tar -xvf Widfly 10.x

Download GenoVault WAR file

Link for the GenoVault war file Click here

Copy Genome-1.jar Jar file from GenoVaul_Jar's folder into the Wildfly deployment folder.

	cp Genome-1.jar ~/wildfly/standalone/deployments/

Change the Database server hostname and port as per user setting.

Get Started

Default Portal Access URL :

http://<Application server>:8080/Genome-1 

By default admin user is created for ADMIN module (password admin). Change the password once logged in and create appropriate users for GenoVault module.

Login as Admin and Change the Cloud Configuration

Standalone Client:

Genovault Standalone Client is enable to transfer the very large files of the user to the Server. To run server downlod the jar file.

Link for the Standalone server and client Click here

Copy the fdt.jar from the Standalone directory to the destination directory

java -jar <JAR file path> [command] [command options]

Run fdt Jar on the Server from the

Example for execution:

java -jar fdt.jar

Stand-alone Usage

GenoVault tool can be executed on a stand-alone desktop machine on which JAVA is installed. Below is the command line usage for the JAVA jar file. Run GenovaultFX-1.jar from the Client machine

java -jar <JAR file path> [command] [command options]

Example for execution:

java -jar GenovaultFX.jar