README.md

In FINNGEN/CohortOperationsShinyApp: CohortOperationsShinyApp

CohortOperationsShinyApp

Javier Gracia-Tabuenca

Intro

The goal of CohortOperationsShinyApp is to provide a graphical interface to create new cohorts based on cohorts imported from Atlas or from a text file.

A cohort in this tool follows the epidemiological definition: “A cohort is a set of persons who satisfy one or more inclusion criteria for a duration of time” [1].

This web app is a graphical interface to other R-packages which provide the underlying functionality. For programming use cases check these:

• FinnGen/FinnGenTableTypes: Provides tools to create and operate cohortData tables.
• FinnGen/CDMTools: Provides connection to Atlas and Atlas’ CDM databases.

This project follows Golem philosophy for the development of Shiny Apps, including modularisation, unit testing, shiny server testing, yalm configuration, and dockerisation. Moreover, this projects uses renv for package dependency management.

For details on the development, testing, and running of the app see detailed documents in dev/.

Running in SandBox

If it is the first time you run the app you need first to download it into SandBox.

Open a terminal inside SandBox. Pull the image :

docker pull eu.gcr.io/finngen-sandbox-v3-containers/cohort_operations_shiny_app:latest

Once the image is available in SandBox you can run the following command Run:

docker run -p 8888:8888 -e BUCKET_SANDBOX_IVM=$BUCKET_SANDBOX_IVM eu.gcr.io/finngen-sandbox-v3-containers/cohort_operations_shiny_app:latest > /home/ivm/cohort_operations_shiny_app.log & sleep 5 && firefox localhost:8888

This should also open Firefox browser. If not, open it and browse to http://0.0.0.0:8888.

Report an Issue

Go to the tab Issues in the GitHub repository.

Click New issue.

Select if you want to file a problem you found "Bug Report", or if you have an idea that will improve the app "Feature request".

FINNGEN/CohortOperationsShinyApp documentation built on Oct. 1, 2023, 12:14 p.m.