Subscribe to important updates on genomic variants of interest, such as changes in ClinVar classification
- Python 3.3+
- mongodb
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
mongod --dbpath /path/to/db
FLASK_APP=wsgi.py flask run --reload
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
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.
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