Podman FDA Submission Pilot 4

Container that runs Shiny Application with Pilot 2 submission

Proof of concept Shiny container by Appsilon based on Pilot 2 from the RConsortium.

Overview

• Builds container image with Pilot 2 for container-based submission
• Easy reproducibility without having to install R environment and packages
  • Using podman-compose the process only needs 1 command
  • Manually building it via podman uses 3 commands
• Based on OpenSource Podman

Installation and Requirements

Refer the installation_guide.md for installation steps for Windows, Mac OSX and [Ubuntu](installation_guide.md#ubuntu

Steps to run the Pilot-4 app

Step 1 - Download / clone the repository

git clone --recurse-submodules https://github.com/Appsilon/experimental-fda-submission-4-podman
cd experimental-fda-submission-4-podman

Step 2 - Run the container locally

There are 2 methods to run the container. Using podman or podman-compose

Step 2A - Creating and running a container via podman

After running the container, the Pilot-4 application can be accessed in the browser at http://localhost:8787.

podman build . --tag experimental-fda-submission-4-podman
podman pod create --publish 8787:8787 --name pilot-pod
podman run -dt --pod pilot-pod experimental-fda-submission-4-podman:latest

Step 2B - Run the container with podman-compose

After running the container, the Pilot-4 application can be accessed in the browser at http://localhost:8787.

podman-compose up -d --pull

Screenshot of the Pilot running

Appendix

Using GitHub Container Registry

The user can use a different container registry from the default docker.io by changing the BUILD ARGS of the docker image. It needs to change the IMAGE_REGISTRY=ghcr.io and IMAGE_ORG=rocker-org to appropriate values. The organization also needs to change as it has different usernames in docker.io (rocker) and ghcr.io (rocker-org).

A preliminary step to login to GitHub registry is required, you can use your own GitHub username and password, or your personal access token (PAT).

podman login ghcr.io --username <your-username-here>

# or if you already a personal access token
echo $PAT | podman login ghcr.io --username <your-username-here> --password-stdin

After login, to change the registry to GitHub you can use one of the methods below:

1. Running podman via command line
2. Edit the Dockerfile file
3. Edit the docker-compose.yml file

1. To build the image in the command line by running:

podman build . --build-arg IMAGE_REGISTRY=ghcr.io --build-arg IMAGE_ORG=rocker-org --tag experimental-fda-submission-4-podman

2. Edit the Dockerfile file by changing the following ARGS:

# ...
ARG IMAGE_REGISTRY=ghcr.io
ARG IMAGE_ORG=rocker-org
# ...

# build the image by running:
# podman build . --tag experimental-fda-submission-4-podman

3. Edit the docker-compose.yml by changing the service.pilot-4-podman.build.args:

ℹ️ note: This can be done by changing the existing example in docker-compose.yml or creating a new service with the different registry.

# edit the lines below
# ...
  build:
    context: .
    args:
      IMAGE_ORG: rocker
      IMAGE_REGISTRY: docker.io
# ...

# build the image using podman-compose by running:
# podman-compose build --pull pilot-4-podman