CReSCENT: CanceR Single Cell Expression Toolkit (Web application) - Developer Documentation

For user manual please go to CReSCENT Docs: https://pughlab.github.io/crescent-frontend/

Prerequisites

• Git (to clone this repo)
• Node.js
• Docker
• docker-compose

Local development

Clone this repo.

Copy sample.env to .env and react/sample.env to react/.env and customize as needed.

npm install to install server dependencies. docker-compose up to start the server backend.

If you are on Windows or Mac, make sure the GRAPHENE_DEV variable in your .env is set to True, and share /var/lib/toil from docker in file sharing. Otherwise, on linux, set GRAPHENE_DEV to False and run docker network connect bridge minio to connect minio to the default network, followed by docker inspect minio to retreive the IP of the container, and finally echo "the ip" > graphene/src/schema/minioIP.txt to give graphene the IP.

In the react folder, npm install for frontend dependencies and then npm start to start a React development server.

git clone https://github.com/suluxan/crescent-frontend.git
cd crescent-frontend
cp sample.env .env
cp react/sample.env react/.env
npm i
docker-compose up -d
# Linux only
# Set GRAPHENE_DEV=False in .env
docker network connect bridge minio
docker inspect minio
# Find the IPAdress under the Network called bridge, not crescent_frontend_default
echo "the ip" > graphene/src/schema/minioIP.txt
# End of Linux only
cd react
npm i
npm start

Deploy to production

Clone this repo.

Copy the SSL certificate files specified in nginx/conf/default.conf to nginx/certs/. Copy sample.env to .env and react/sample.env to react/.env and customize as needed. The GRAPHENE_DEV variable should be set to False.

npm install to install server dependencies. In the react folder, npm install for frontend dependencies and then npm build to compile a release version of the frontend in build.

In the root folder, docker-compose -f docker-compose.yaml -f docker-compose.prod.yaml up or npm start to start an HTTPS nginx reverse proxy for the entire application.

git clone https://github.com/suluxan/crescent-frontend.git
cd crescent-frontend
mkdir nginx/certs
cp YOUR_CERTIFICATES_HERE nginx/certs
cp sample.env .env
cp react/sample.env react/.env
npm ci
cd react
npm ci
npm run build
cd ..
docker-compose -f docker-compose.yaml -f docker-compose.prod.yaml up -d 
docker network connect bridge minio
docker inspect minio

Now copy the IPAddress under Networks: bridge NOT Networks: crescent_frontend_default near the bottom. Excluding the quotations.

echo "the ip" > graphene/src/schema/minioIP.txt