WebSTR web browser (front-end)
This repository contains code and instructions for WebSTR - web browser of Human genome-wide variation in Short Tandem Repeats (STRs). Our goal is to make large STR genotype datasets used by the broader genomics community by facilitating open access to this data.
WebSTR is the result of collaboration between two scientific groups Maria Anisimova’s Lab and Melissa Gymrek’s Lab.
Source code for the WebSTR-API can be found here: https://github.com/acg-team/webSTR-API
Instructions on how to set-up WebSTR web app locally (for development)
Set up python3 and virtualenv on your machine:
For Mac, follow instructions here.
Create new virtual env with python3 and install all the requirements with the following command:
pip install -r requirements.txt
Copy data files to data directory
We provide neccesssary data files upon request and currently working on incorporating them fully into the backend.
You will need:
- dbSTR.db (contains older panels mapped to hg19 assembly)
- hg19.fa and hg19.fai
- hg38.fa and hg38.fai
Start web server
To run for testing and development:
export DATAPATH=*full data directory path*
python ./WebSTR/WebSTR.py --host 0.0.0.0 --port <port>
For production mode, we use gunicorn + nginx.
WebSTR Backend - database and API
By default WebSTR will be using WebSTR-API hosted on our server. If you would like to set up the database and WebSTR backend as well (for example if you would like to make a new endpoint or add your own data to the database), please follow instructions to set up WebSTR database and API locally provided here https://github.com/acg-team/webSTR-API. Proceed then to modify API_URL variable in WebSTR browser so the app communicates with your local instance of WebSTR-API.