EasyNGS provide a rich and interactive web application for NGS data processing. EasyNGS can process and browse remote big data from OpenCGA server such as Fastq, BAM and VCFs files. It can also display data from CellBase.
You can find EasyNGS documentation and tutorials at: https://github.com/opencb/easyngs/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.
EasyNGS is versioned following the rules from Semantic versioning.
We recommend to contact EasyNGS developers by writing to OpenCB mailing list opencb@googlegroups.com. The main developers and maintainers are:
- Ana Conesa (aconesa@cipf.es)
- Ignacio Medina (im411@cam.ac.uk)
- Pedro Furio (pfurio@cipf.es)
- Nicolás Lucero (nicolas_lucero85@yahoo.es)
EasyNGS is an open-source and collaborative project. We appreciate any help and feeback 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.
EasyNGS is developed using Polymer and HTML5, therefore it is mainly developed in JavaScript and makes a heavy usage of HTML and CSS. It uses Bower as building tool. EasyNGS also requires of OpenCB JSorolla to be built, this is a JavaScript library developed for several OpenCB web-based projects, this can be found as Git submodule in EasyNGS.
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 EasyNGS from OpenCB is JSorolla. EasyNGS master branch depends on stable branches in JSorolla, while develop branch of EasyNGS depends on JSorolla develop.
The following technologies are needed to build EasyNGS: Node.js, npm and Bower.
To install Node.js you can visit this link.
npm stands for node packaged modules and it is the dependency manager of Node.js.
After installing Node.js and npm, we can install Bower by executing the following commands with root permission:
sudo npm install -g bowerEasyNGS is an open-source and free project, you can download develop branch by executing:
$ git clone https://github.com/opencb/easyngs.git
Cloning into 'easyngs'...
remote: Counting objects: 2274, done.
remote: Compressing objects: 100% (16/16), done.
remote: Total 2274 (delta 5), reused 0 (delta 0), pack-reused 2256
Receiving objects: 100% (2274/2274), 12.01 MiB | 678.00 KiB/s, done.
Resolving deltas: 100% (952/952), done.
To fetch the latest stable release at master branch can be downloaded executing:
$ git clone -b master https://github.com/opencb/easyngs.git
Cloning into 'easyngs'...
remote: Counting objects: 2274, done.
remote: Compressing objects: 100% (16/16), done.
Receiving objects: 13% (296/2274)
remote: Total 2274 (delta 5), reused 0 (delta 0), pack-reused 2256
Receiving objects: 100% (2274/2274), 12.01 MiB | 507.00 KiB/s, done.
Resolving deltas: 100% (952/952), done.
After this, in both cases, you must execute the following command to fetch the JSorolla submodule:
git submodule update --init
After install Node.js and npm we have to install npm packages for EasyNGS, from the the root folder execute:
npm installThis will make npm to look at file package.json and install locally all the dependencies listed there.
To install all Bower dependencies for EasyNGS execute from the root folder:
bower installThis will make Bower to look at file bower.json and install locally all the dependencies.
First, you must update JSorolla dependencies:
cd lib/jsorolla
npm install
bower installFinally, to build EasyNGS execute:
npm run buildWhen 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 EasyNGS.
JetBrains is supporting this open source project with:
