GeneSetCart

This is an application for assembling, augmenting, combining, visualizing and analyzing gene sets: genesetcart.cfde.cloud

Getting Started

# go to app (imagineset) directory
cd imagineset
# prepare .env file & review
cp .env.example .env
# start database
#  (NOTE: If you're running another postgres database on your system, you should turn it off as the ports will conflict)
docker-compose up -d g2sg-postgres
# install node modules
npm i
# initialize prisma
npx prisma migrate deploy
# run dev server
npm run dev

Open http://localhost:3000 with your browser to see the platform.

.env File Set Up

For the NEXTAUTH_SECRET value Run

openssl rand -base64 32

Set NEXTAUTH_URL=http://localhost:3000

Running the python backend

To run the python backend. Run the command:

gunicorn --workers 2 --timeout 600 --bind 0.0.0.0:8000 app:app

And set PYTHON_API_BASE='http://0.0.0.0:8000' in the .env file

Provisioning the Database

To use the site, you have to populate your local database with gene and crossing pairs data. Firstly, make sure apply migrations to create the tables

# go to app (imagineset) directory
cd imagineset
npx prisma migrate deploy

and then run ingest script in database directory to add the data to these tables

# go to database directory (use the following commands if in imagineset directory):
cd ..
cd database
# download requirements
pip install -r requirements.txt
# prepare .env file containing DATABASE_URL
cp .env.example .env
# run ingest script
python3 ingest.py