scNavigator

scNavigator is a docker-compose application: server-side contains of multiple containers like webserver written in Kotlin and file system manager written in Python

Navigator: server-side

Server side is built using ./gradlew build (to get jars) and docker-compose.

We have several main services:

• Nginx
• MongoDB
• Kotlin-based backend server
• Python-based h5-converter and file system manager

To build the application first run:

./gradlew build

This will run kotlin-based applications tests and builds.

Then run:

docker-compose build (with sudo if required)

this will build the whole multi-container application and also run python tests.

Navigator: client-side

Frontend for Navigator is build with React + Redux which allows full control over the application state at any point. Frontend is build locally outside of docker-compose container. Building frontend outside of docker-compose container allows us fix client-side bugs and improve client-side behaviour without stopping/restarting docker-compose application.

You can build client side using npm utils:

cd ./scn_js
npm install
npm run build

Datasets

If you want your datasets to show up in Navigator, you have to prepare them in a h5ad format with some extra fields to uns.

Prepare your datasets locally in one folder and make sure to change DATASET_PATH in .env to this folder you chose. Also make sure that TMP_PATH from .env exists: there Navigator will store datasets in internal format.

Running Navigator locally

To run Navigator locally you will first need to build Navigator server-side. Then build client-side js code and then just start docker-compose. Be careful, docker-compose might require sudo privileges.

## building server-side
./gradlew build
docker-compose build

## building client-side
cd ./scn_js
npm install
npm run build
cd ..

## running multi-container

docker-compose up

## running multi-container detached

docker-compose up -d