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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.
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.
Install Node.js and npm
After installing Node.js and npm, we can install Bower by executing the following commands with root permission:
sudo npm install -g bower
To install grunt, run
sudo npm install -g grunt-cli
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:
git clone https://github.com/opencb/iva.git
Latest stable release at master branch can be downloaded by executing:
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):
git submodule update --init
Go to lib/jsorolla and checkout to next-v2.0.0 branch of Jsorolla and do the following:
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:
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:
This will make Bower to look at file bower.json and install locally all the dependencies.
At last execute:
When completed, all compiled files will be located under the build folder.
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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