Overview

IVA is a generic Interactive Variant Analysis browser that can be used for the visualization of biological information from various data sources. IVA uses data from OpenCGA which is an OpenCB project.

Documentation

You can find IVA documentation and tutorials at: https://github.com/opencb/iva/wiki.

Issues Tracking

You can report bugs or request new features at GitHub issue tracking.

Release Notes and Roadmap

Releases notes are available at GitHub releases.

Roadmap is available at GitHub milestones. You can report bugs or request new features at GitHub issue tracking.

Versioning

IVA is versioned following the rules from Semantic versioning.

Maintainers

We recommend to contact IVA developers by writing to OpenCB mailing list opencb@googlegroups.com. The main developers and maintainers are:

Ignacio Medina (im411@cam.ac.uk) (Founder and Project Leader)
Javier Perez Florido (javier.perez.florido.ext@juntadeandalucia.es)
Alexis Martínez (alexis.martinez@juntadeandalucia.es)

Former Contributors

Swaathi Kandasaamy (sk913@cam.ac.uk)
Asuncion Gallego (agallego@cipf.es)

Contributing

IVA is an open-source and collaborative project, currently developement is mainly carried out by Stefan Gräf and Ignacio Medina teams from the University of Cambridge and Joaquin Dopazo team from CIBERER. We appreciate any help and feedback from users, you can contribute in many different ways such as simple bug reporting and feature request. Dependending on your skills you are more than welcome to develop client tools, new features or even fixing bugs.

How to build

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 of OpenCB JSorolla project to be built, this is a JavaScript library developed for several OpenCB web-based projects, this can be found as Git submodule in IVA.

Stable releases are merged and tagged at master branch, you are encourage to use latest stable release for production. Current active development is carried out at develop branch, only building is guaranteed and bugs are expected, use this branch for development or for testing new functionalities. The only dependency of IVA from OpenCB is JSorolla.

Prerequisites

The following technologies are needed to build IVA: Node.js, npm and Grunt.

Installing 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.

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:

$ git clone https://github.com/opencb/iva.git
Cloning into 'iva'...
remote: Counting objects: 624, done.
remote: Total 624 (delta 0), reused 0 (delta 0), pack-reused 624
Receiving objects: 100% (624/624), 139.37 KiB | 0 bytes/s, done.
Resolving deltas: 100% (356/356), done.
Checking connectivity... done.

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

$ git clone -b master https://github.com/opencb/iva.git
Cloning into 'iva'...
remote: Counting objects: 624, done.
remote: Total 624 (delta 0), reused 0 (delta 0), pack-reused 624
Receiving objects: 100% (624/624), 139.37 KiB | 191.00 KiB/s, done.
Resolving deltas: 100% (356/356), done.
Checking connectivity... done.

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 develop branch of Jsorolla by

cd lib/jsorolla
git checkout develop

Build

First, you must update JSorolla dependencies, from the root folder execute:

cd lib/jsorolla
npm install

Finally, to build IVA execute:

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

npm install

And now execute:

npm run build

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

Testing

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

Execute Tests in development with nightwatch(http://nightwatchjs.org/)

Prerequisite: make sure you have JDK installed, with at least version 8. If you don't have it, you can grab it from http://www.oracle.com/technetwork/java/javase/downloads/index.html.

npm install --dev
Selenium server. Download the latest release .jar from http://selenium-release.storage.googleapis.com/index.html. i.e. selenium-server-standalone-3.7.0.jar
Chromedriver. Download from https://sites.google.com/a/chromium.org/chromedriver/downloads that version which supports your chrome versión. You can review what version fits your browser here https://chromedriver.storage.googleapis.com/2.33/notes.txt.
Create a bin folder inside your test folder in root path
Move selenium bin and chrome bin inside that bin folder.
npm run test-e2e ( or ./node_modules/.bin/nightwatch test/e2e/clinical-prioritization.js if you want execute just one)

alemarcha / iva