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Last pushed: 5 months ago
Short Description
VDJServer Webapp
Full Description

VDJServer Backbone

VDJServer Backbone is a next generation immune repertoire analysis portal.


##Development Guidelines

Code Style

  • Code should roughly follow Google Javascript Style Guide conventions:

  • A jscs.rc file (Javascript Code Style Checker) file has been provided in the project repo for any developers who use it.

  • A git pre-commit hook is available via the file To use it, just symlink it as follows: ln -s ../../ .git/hooks/pre-commit

  • Spaces are preferred over tabs, and indentation is set at 4 spaces.

  • Vimrc settings: set shiftwidth=4, softtabstop=4, expandtab

Git Structure

  • This project uses the Git Flow methodology for code management and development:

  • New development and features should be done on branches that are cloned from the develop branch, and then merged into this branch when completed. New release candidates should be branched from develop, and then merged into master once they have been tested/verified. Once a release branch is ready for production, it should be merged into master and tagged appropriately.

##Development Setup

- Clone project
git clone

cd [project location]/component

- Install node.js
# Mac OS X (assuming that the homebrew package manager is already installed)
brew install node

# Debian
sudo apt-get install nodejs nodejs-legacy

- Install compass/sass dependencies
# Mac OS X
sudo gem install sass compass

# Debian
sudo apt-get install ruby ruby-dev && sudo gem install sass compass

- Install global npm modules
npm install -g bower grunt grunt-cli

- Pull npm dependencies
npm install

- Pull bower dependencies
bower install

- Setup local environment config file
cd [project location]/docker

cp environment-config/environment-config.js.defaults environment-config/environment-config.js

vim environment-config/environment-config.js

- Start local instance
cd [project location]/component

grunt server

##Running through docker

The vdj-backbone project can be run through docker in two ways:

A.) Using a prebuilt image:


B.) Building a local image

You will need to create a local environment-config file with either option. A sample config file is available in this repository at "component/app/scripts/config/environment-config.js.defaults".

cp docker/environment-config/environment-config.js.defaults ~/environment-config.js

vim ~/environment-config.js

Using a prebuilt image

After the config is set up, you can run the image as follows:

docker run -t -p 9001:9001 -v ~/environment-config.js:/var/www/html/vdjserver-backbone/app/scripts/config/environment-config.js vdjserver/backbone:release-1 grunt server --force

You can also mount your source code directory in the container if you would prefer to make code changes:

cp ~/environment-config.js [vdjserver-backbone repo location]/component/app/scripts/config/

docker run -t -p 9001:9001 -v $(pwd)/component:/var/www/html/vdjserver-backbone vdjserver/backbone:release-1 bash -c "bower install && npm install && grunt server --force"

Building a local image for development

cp ~/environment-config.js [vdjserver-backbone repo location]/component/app/scripts/config/

cd [vdjserver-backbone repo location]

docker build -t vdj-dev .

docker run -t -p 9001:9001 -v $(pwd)/component:/var/www/html/vdjserver-backbone vdj-dev bash -c "bower install && npm install && grunt server --force"
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