Genome Maps is a modern and high-performance web-based HTML5 genome browser. Genome Maps can browse data from CellBase and render remote big data from OpenCGA server such as BAM and VCFs files.

Genome Maps constitutes the genome browser component of OpenCB for CellBase and OpenCGA data visualization. It is used by other OpenCB projects such as OpenCGA as well as other external applications such as ICGC or Babelomics.

Note: This repository is a major refactoring of https://github.com/opencb-bigdata-viz/genome-maps. All users must update to this one.

You can find Genome Maps documentation and tutorials at: https://github.com/opencb/genome-maps/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.

Genome Maps is versioned following the rules from Semantic versioning.

We recommend to contact Genome Maps 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)
• Susi Gallego (sgaort@gmail.com)

• Francisco Salavert (fsalavert@cipf.es)

Genome Maps 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.

Genome Maps is developed in HTML5, therefore it is mainly developed in JavaScript and makes a heavy usage of HTML and CSS. It uses Bower as building tool. Genome Maps 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 Genome Maps.

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 Genome Maps from OpenCB is JSorolla. Genome Maps master branch depends on stable branches in JSorolla, while develop branch of Genome Maps depends on JSorolla develop.

The following technologies are needed to build Genome Maps: 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 bower

Genome Maps is an open-source and free project, you can download develop branch by executing:

$ git clone https://github.com/opencb/genome-maps.git
Cloning into 'genome-maps'...
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/genome-maps.git
Cloning into 'genome-maps'...
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 Genome Maps, from the the root folder execute:

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 Genome Maps execute from the root folder:

bower install

This 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 install

Finally, to build Genome Maps execute:

npm run build

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 Genome Maps.

JetBrains is supporting this open source project with:

[] (http://www.jetbrains.com/idea/)