F1000Research/genemania

GeneMANIA

http://genemania.org

GeneMANIA helps you predict the function of your favourite genes and gene sets. Build instructions General

Requirements:

JDK Maven

Projects:

common : common APIs used amongst the projects engine : the GeneMANIA algorithm engine broker : for communicating between the website and workers that use the engine website : the website backend (webservices etc) adminweb : the administrative interface for editing data used in the website plugin : the Cytoscape plugin/app

Building:

To build all Java projects: mvn package To build a particular project, e.g. website mvn package -pl website -am

Website UI

Notes:

The website-ui contains the frontend interface for the website. Naturally, JavaScript is used for the UI and the build process, so the build process here differs from the previous Java projects. The website should pull in the latest UI by calling the appropriate website-ui target — that way, the website always automatically gets the latest UI on each build. The website UI assumes a local development environment, unless deployed to the website Java project. For local development, the UI assumes the website server resides at http://localhost:8080/genemania. You can configure this in js/conf.js.

Requirements:

Node.js & npm Gulp: sudo npm install -g gulp NB: you must npm install before using gulp

Targets: gulp ...

website : deploy to the website Java project websiteclean : clean the web directory for the website Java project minify : build a local minified UI for debugging clean : cleans the website UI so it is in a fresh state for local debugging refs : updates file references when you add JS, CSS, etc (useful during development)

Deployment instructions Deploying a local copy of the website

TODO TODO

Funding

GeneMANIA is actively developed at the University of Toronto, in the Donnelly Centre for Cellular and Biomolecular Research, in the labs of Gary Bader and Quaid Morris. GeneMANIA development was originally funded by Genome Canada, through the Ontario Genomics Institute (2007-OGI-TD-05) and is now funded by the Ontario Ministry of Research and Innovation.