docker/README-Docker.md

In ohdsi-studies/PioneerWatchfulWaiting: PIONEER / EHDEN / OHDSI prostate cancer study

Docker container instructions

This folder contains a number of files that can help you to run the study package within a Docker container. Ready-to-go containers are also published on Docker Hub.

Instructions

These instructions assume you would like to use the published container, but of course you can also choose to build it from source yourself using the provided Dockerfile.

1. Supply configuration variables and create the cointainer

You can use the file pioneer-package.env in this folder to update environment variables needed to run the study. Please copy it to a file named .env and fill in your details. You can then create and start the container using the following command:

docker run -itd --env-file .env --name pioneer keesvanbochove:pioneer-package

Note that depending on your Docker configuration you may need to add other arguments, such as the target network.

2. Copy your private SFTP upload key to the container

docker cp study-data-site-pioneer pioneer:/

3. Run the study

You can use the following command to attach to the R session started within the container:

docker attach pioneer

You can now follow the instructions in extras/CodeToRun.R from section 2 on as if you were running locally.

A few comments: If you want to temporarily return to your command line but keep the container running, the default detach sequence is CTRL-p CTRL-q Please don't forget to run the uploadDiagnosticsResults and uploadStudyResults commands to upload to the OHDSI SFTP server! This requires your container to have internet connection. * If you exit the R session (using q()), the container will be stopped, so don't do that until you are finished.

4. Copy the results out of the container onto your filesystem

By default, the results are in a folder named identical to your database ID. So if your database ID is SP and you would like to copy the result folder to your current path, you would run:

docker cp pioneer:/SP .

1. Destroy the container After you copied and inspected the results, you can safely destroy the container. However, this will not delete the results in the result tables in your database (see COHORT_SCHEMA).

docker rm pioneer

ohdsi-studies/PioneerWatchfulWaiting documentation built on June 2, 2022, 4:06 a.m.