Variant Subscription Service (VSS)
Subscribe to important updates on genomic variants of interest, such as changes in ClinVar classification
Setup
Prerequisites
- Python 3.3+
- mongodb
Installation
git clone https://github.com/buske/variant-subscription-service.git
cd variant-subscription-service
virtualenv -p python3 .virtualenv
source .virtualenv/bin/activate
pip install -r requirements.txt
Run server
Start mongodb
mongod --dbpath /path/to/db
Run in development mode
FLASK_APP=wsgi.py flask run --reload
Run in production mode
Instructions for Ubuntu 16.04
- Install nginx
- Set up nginx
sudo cp deploy/vss.nginx /etc/nginx/sites-available/vss
sudo ln -s /etc/nginx/sites-available/vss /etc/nginx/sites-enabled/
systemctl restart nginx
- Set up uWSGI service
sudo cp deploy/vss.service /etc/systemd/system/vss.service
sudo systemctl start vss
sudo systemctl enable vss
- Override necessary environment variables in
production.cfg
(exclude from VCS)
cp config.py production.cfg
nano production.cfg
- Define environment variable
VSS_SETTINGS
with the FULL path to this cfg file, e.g.VSS_SETTINGS=/path/to/production.cfg
Import ClinVar data
Fetch source data
Soon, you will be able to fetch the latest source data with vss-dat-import
In the meantime, you must parse the ClinVar data yourself using the Macarthur Lab parser. As of 15 Sept 2017, you must use the unmerged pr/33. The clinvar_alleles.single.b37.tsv.gz
file is what is required by the importer.
Import parsed ClinVar data
You can then run the importer periodically (by hand or crontab) to notify users of changes to ClinVar classifications:
VSS_SETTINGS=/path/to/production.cfg python -m vss.scripts.import /path/to/clinvar_alleles.single.b37.tsv.gz