A web-app that visualizes genomic context data provided by third party services.
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README.md

README.md

Genomic Context Viewer

The Genomic Context Viewer (GCV) is a web-app that visualizes genomic context data provided by third party services. Specifically, it uses gene family assignment as a unit of search and comparison. By adopting a common set of gene families, data-store operators can deploy federated instances of GCV.

This repository contains GCV itself (the client) and a basic server that demonstrates how the RESTful API GCV depends on can be implemented.

User docs, the services API, and non-legume examples are available in the Wiki.

Running GCV

GCV is a standalone web-app that can be run locally on a personal computer or integrated into a website. To run GCV locally, open index.html in a web-browser. By default, GCV retrieves data from the Legume Information System. See the wiki for more information on how to retrieve data from other sources, and for instructions on general use.

Running the Server

The example server is implemented in Django 1.8.6 and Python 2.7. The easiest way to run the server locally is to create a Python Virtual Environment. Once Python virtual environments is installed, you can create a virtual environment as follows

virtualenv -p /usr/bin/python2.7 venv

You can then activate the environment

. ./venv/bin/activate

All the server's dependencies are listed in the requirements.txt file, which can be used to bootstrap the virtual environment as follows

(venv) pip install -r requirements.txt

The server is designed to use a PostgreSQL database configured with an extended version of the Chado schema. See the wiki for details on the necessary extensions.

Lastly, the server loads the database credentials and the secret key from environment variables: PGNAME, PGUSER, PGPASSWORD, PGHOST, PGPORT, SECRET_KEY .

Once configured, the server can be run locally as follows

python manage.py runserver

This command should only be used for running a local instance of the server. See the Django docs for deployment options. By default, GCV is configured to retrieve data from the Legume Information System. See the wiki for information on how to retrieve data from your own instance of the server.