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OpenCGA vs IVA

OpenCGA is an open-source project that aims to provide a Big Data storage engine and analysis framework for genomic scale data analysis of hundreds of terabytes or even petabytes. OpenCGA provides a scalable and high-performance Storage Engine framework to index biological data such as BAM or VCF files using different NoSQL databases. A metadata Catalog has been also developed to provide authentication and ACLs and to keep track all of files and sample annotation. All these can be queried through a comprehensive RESTful web services API or using the command line interface.

To set up OpenCGA, Please go to Installation Guide.

IVA is a generic Interactive Variant Analysis browser that can be used for the visualization of biological information from various data sources. IVA queries OpenCGA server through web services and serves as a visualization tool. 

Getting IVA

IVA can be set up either by downloading build.tar from every stable release of IVA which can be found in https://github.com/opencb/iva/releases or by building it from scratch and then copying the build content into a web server like Apache HTTP Server.

Build software

IVA is developed in HTML5, therefore it is mainly developed in JavaScript and makes a heavy usage of HTML and CSS. It uses Grunt as building tool. IVA also requires OpenCB JSorolla project to be built, which is a JavaScript library developed for several OpenCB web-based projects.  This can be found as Git submodule in IVA.

Prerequisites

The following technologies are needed to build IVA: Node.jsnpmBower and Grunt.

Install

Node.js and npm

To install Node.js you can visit this link.

npm stands for node packaged modules and it is the dependency manager of Node.js.

Install Bower

After installing Node.js and npm, we can install Bower by executing the following commands with root permission:

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sudo npm install -g bower
Install Grunt

To install grunt, run

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sudo npm install -g grunt-cli

Cloning

IVA is an open-source project and can be downloaded either as package(tar.gz) from GitHub releases or source code by cloning the repository.

Default develop branch can be downloaded by executing:

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git clone https://github.com/opencb/iva.git

Latest stable release at master branch can be downloaded by executing:

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git clone -b master https://github.com/opencb/iva.git

After this, in both cases, you must execute the following command to fetch the JSorolla submodule (only the first time):

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git submodule update --init

Go to lib/jsorolla and checkout to next-v2.0.0 branch of Jsorolla and do the following:

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cd lib/jsorolla
git checkout next-v2.0.0
npm install 
bower install
grunt

Finally, to build IVA execute:

We have to install npm packages for IVA, from the the root folder execute:

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npm install

This will make npm to look at file package.json and install locally all the dependencies listed there.

To install all Bower dependencies for IVA execute from the root folder:

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bower install

This will make Bower to look at file bower.json and install locally all the dependencies.

At last execute:

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grunt

When completed, all compiled files will be located under the build folder.

Install

You can copy build content to a web server such as Apache HTTP Server and open your favourite internet browser to open IVA.





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