RNA-seq-web

A web tool for browsing publicly available RNA-seq datasets and derived co-expression networks. Here is a running instance with brain data.

Development

Want to contribute in developing the website? Awesome.

Clone the repo

git clone https://github.com/Nealelab/rna-seq-web
cd rna-seq-web

Install requirements

Install Python packages (you should have Python 3 and pip3 installed):

pip3 install -r requirements.txt

If you don't have Node, install it.

Install npm packages:

npm install

Run webpack

Run webpack in watch mode so it recreates the JavaScript bundle every time you make changes to the sources:

node_modules/webpack/bin/webpack.js --config webpack.dev.js --watch

The bundle file appears in static/bundle.js

Run a development server

To use the Flask dev server:

export FLASK_ENV=development
python3 app.py

Develop

To work on the Flask backend, start from app.py. To work on the React frontend, start from js/app.js.

Deployment in Google Cloud

First, install Docker, Cloud SDK and kubectl.

Create a Docker image

docker build -t gcr.io/DESIRED/TAG:VERSION -f docker/Dockerfile .

Replace DESIRED TAG VERSION with the desired tag and version.

Push the image to Google Container Registry:

gcloud docker -- push gcr.io/DESIRED/TAG:VERSION

Authenticate to Google Cloud

gcloud auth login

Create a container cluster

gcloud container clusters create rna-seq-web --num-nodes=1 --machine-type=n1-standard-1 --zone=us-east1-b

The application currently keeps all data in RAM - the machine type should have enough memory for this. Currently a regular 1 CPU / 3.75 GB machine is enough when one worker thread is used.

Set up Kubernetes

Create a static, global IP address to use:

gcloud compute addresses create whatever-ip --global

And change kubernetes.io/ingress.global-static-ip-name in k8s/ingress.yaml to whatever-ip.

Change the disk (pdName) in k8s/pv.yaml to one with the wanted data files. Also make sure the disk size ("storage" attributes) is the actual size. Make sure config.py matches the locations of the data on the disk.

Change image in k8s/ss.yaml to the Docker image you created. Change the memory attributes as needed. Make sure mountPath matches the data locations in config.py and that storage is the correct size.

Finally, create the Kubernetes setup:

kubectl apply -f k8s/ingress.yaml  
kubectl apply -f k8s/pv.yaml  
kubectl apply -f k8s/ss.yaml

After kubectl get pods shows a running pod, visit the IP address you created (use kubectl get ingress to find the address). For Kubernetes troubles, try kubectl get events --sort-by=.metadata.creationTimestamp, kubectl describe pod PODNAME, and kubectl logs PODNAME, where PODNAME is the pod name from kubectl get pods.