Deployment

Docker

Prerequisites

Before you begin, make sure you have installed the following tools:

docker (>=20.10)
docker-compose (>=1.27)

Create a docker-compose file

Create an empty file called docker-compose.yml, and copy the following code into file.

version: '2'
services:
    adifa:
        image: haniffalab/adifa:latest
        container_name: adifa
        entrypoint: sh
        command: ./boot-autodiscover.sh
        ports:
        - 5000:5000
        volumes:
        - ./path/to/your/h5ad:/data
        environment:
        - "DATA_PATH=/data"

Replace haniffalab/adifa:latest with your preferred image tag (see below)
Replace /path/to/your/h5ad with the path to the directory where your .h5ad files are located
Remove the entrypoint and command directives to prevent autodiscovery during the service boot
Map the service to a different port on the host machine, for example - 5000:80 to serve on port 80

Start the docker service

Run the following command in the same directory:

docker-compose up

This command will load the Adifa application, read your .h5ad files and start the web server. Depending on the size of your data files, the application may take several minutes to load.

To access the application, open http://localhost:5000 in a browser.

Offical Docker images

You can pull the official Adifa Docker images from the DockerHub Haniffa Lab

The latest tag can be used for the most recent

docker pull haniffalab/adifa:latest

The dev tag can be used for the most recent

docker pull haniffalab/adifa:dev

Building your own custom docker images

You can build a custom image from the root of the sc-afida repositry

docker build -t davehorsfall/adifa-custom:latest .

docker-compose

This is then the docker-compose.yml so we see it.

version: '2'
services:
# Web server
nginx:
    image: nginx:latest
    container_name: nginx
    volumes:
    - ./nginx.conf:/etc/nginx/conf.d/default.conf
    ports:
    - 80:80
    - 443:443
# Application
adex:
    image: davehorsfall/cellatlas-api:merge
    container_name: adex
    volumes:
    - ./data:/data
    ports:
    - 5000:5000
    environment:
    - "DATA_PATH=/data"
    links:
    - nginx

Nginx

This is then the conf.conf so we see it.

version: '2'
services:
# Web server
nginx:
    image: nginx:latest
    container_name: nginx