README

These are the steps to set up a containerized docker version of our single cell analysis apps. Shiny apps run using the shinyproxy service which itself will be containerized so that the whole operation can be run on a host system with minimal institutional support. 

1. build the shinyapp docker image: `docker build -f Dockerfile.shinyapp --build-arg GITHUB_PAT=$PAT -t whtns/seurattools:latest .`

	* if troubleshooting package install run: `docker build -f Dockerfile.shinyapp --build-arg GITHUB_PAT=$PAT -t whtns/seurattools:latest . --build-arg CACHEBUST=$(date +%s)`

2. create a docker network called seuratTools-network: `sudo docker network create seurattools-net`

3. edit the application.yml file to refer to the appropriate docker images and containers 
  - id: seuratApp
    container-cmd: ["R", "-e", "shiny::runApp('/root/dockerapp')"]
    container-image: whtns/seurattools
    access-groups: scientists
    container-volumes: ["/dataVolume/storage/single_cell_projects/shinyproxy/dockerdata:/root/dockerdata"]
    container-network: seurattools-net

4. build the shinyproxy docker image `docker build -f Dockerfile.shinyproxy -t whtns/seurattools_container:latest .`

5. run the shinyproxy docker image with `sudo docker run -v /dataVolume/storage/single_cell_projects/shinyproxy/dockerdata:/root/dockerdata -v /var/run/docker.sock:/var/run/docker.sock:ro --group-add $(getent group docker | cut -d: -f3) --net seurattools-net -p 8080:8080 whtns/seurattools_container`