The Interactive Variant Analyser (IVA) is the web user interface for OpenCGA that provides unprecedented features for real-time interaction with genomic data. It is suitable for any scale; from the detailed interpretation of a single genomic test through to assessing the genetic diversity of hundreds of thousands of aggregated genomes. It is not just for bioinformaticians; it provides simple and convenient access for biomedical researchers and clinical scientists as well.
You can find IVA documentation and tutorials at: https://github.com/opencb/iva/wiki.
You can report bugs or request new features at GitHub issue tracking.
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.
IVA is versioned following the rules from Semantic versioning.
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)
- Antonio Altamura (antonio.altamura@genomicsengland.co.uk)
- Javier Perez Florido (javier.perez.florido.ext@juntadeandalucia.es)
- Alexis Martínez (alexis.martinez@juntadeandalucia.es)
- Swaathi Kandasaamy (sk913@cam.ac.uk)
- Asuncion Gallego (agallego@cipf.es)
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.
IVA is mainly developed in JavaScript. It requires of OpenCB JSorolla project to be built, this is a JavaScript library developed for several OpenCB web-based projects, it 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.
To run and build IVA you need: Node.js and npm.
To install Node.js you can visit this link.
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: Enumerating objects: 126, done.
remote: Counting objects: 100% (126/126), done.
remote: Compressing objects: 100% (72/72), done.
remote: Total 10370 (delta 70), reused 85 (delta 38), pack-reused 10244
Receiving objects: 100% (10370/10370), 4.70 MiB | 61.00 KiB/s, done.
Resolving deltas: 100% (6064/6064), 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
npm run install
To run IVA in dev mode (hot reload for CSS files and hot restart (aka live reloading) for JS scripts), run
npm run serve.
To buil IVA, just run
npm run build.
We use Cypress.io as testing framework.
Having the project running through the command npm run serve, you can run the interactive E2E test suite by running the command
npm run e2e
To run test in headless version (no browser) and generate a report, run
npm run e2e-report
for more help, try npm run e2e-report -h.
For Windows environment, just add the suffix -win
npm run e2e-win
npm run e2e-report-win
for more help, try npm run e2e-report-win -h.
The HTML report will be generated in ./report. The filename will have the structure <OPENCGA_STUDY_FQN>__<TIME>_<DATE>.html
