The 4D Genome Browser is a toolkit for querying and visualizing genomics data through the web. It consists of a few different components:
Data is formatted into "projects". A project consists of all of the input data files and a project.json
file describing the files along with settings for viewing them. A project can then be "compiled", having all of its data incorporated into an SQLite database. This database is what the web server queries to serve data. A "release" of a project consists of a copy of the server code, the projectg directory, the project database, static files (including a minified version of the javascript library) along with a copy of the python library for querying the server.
Initialize Python and npm:
# Create a python virtual environment
python3 -m venv venv/
source venv/bin/activate
pip3 install -r requirements.txt
# Init npm
cd client-js/
npm install
./bin/make_release <project>
python3 release/<project>/server/gtkserver.py --port 8000
For example, to run the test.01
project in this repository:
./bin/make_release test.01
python3 release/test.01/server/gtkserver.py --port 8000
From there, open a web browser to localhost:8000
to view the project page:
Clicking on the grey zone or the image of the app will take you to the running instance: