1. Su Lab
  2. BioGPS
  3. biogps_core

Overview

README

Please note that this repo has been migrated to Github. DO NOT develop or post issues on Bitbucket. Thank you!

Please see the BioGPS_core repository on Github




BioGPS - the Gene Annotation Portal

This file tree contains the source code for the user-facing web application portion of BioGPS. It is written in Python and based primarily on Django.

In order to run a complete installation of BioGPS, several separate components are required:

  • BioGPS UI (this project)
  • MyGene.info (gene annotation data)
  • ElasticSearch
  • PostgreSQL

Installation

You can follow this step-by-step instruction to setup a working folder to run BioGPS for development purpose.

The following are the all dependencies needed:

Baseline Required Software

  • Python 2.6+
  • mercurial (for checking out his repo)
  • Java JRE 1.6+ (for JS minification)
  • NodeJS 0.2.6+ (for LESS compilation)

Python Packages

Extra Python software is required for a production installation, documented in "requirements.txt" and installed via pip:

pip install -r requirements.txt

Additional Python software for development (optional) is documented in "optional_dev.txt":

pip install -r optional_dev.txt

Javascript dependencies

  1. ExtJS v3.3.0

Download from this link, and then extract full ExtJS package (not just ext-all.js) to src/assets/js/ext/3.3.0 folder (need to "mkdir src/assets/js/ext" first).

  1. ExtJS plugin ManagedIFrame

Download from this link, and then extract two files: miframe.js and miframe-debug.js to src/assets/js/ext/plugins folder.

Credits

Active Developers

  • Chunlei Wu
  • Ian MacLeod
  • Andrew Su

Past Contributors

  • Marc Leglise
  • Camilo Orozco
  • James Goodale
  • Jason Boyer