Docker Shiny Container

This repository allows to run Shiny in a docker container. This image can be used to integrate Shiny into Galaxy. A variety of different packages are pre-installed and can be used right away.

Context
Galaxy Interactive Environment installation
How to use this Docker image
- From the pre-built image
- Build the image locally
How to interact with Galaxy
Application list

Context [toc]

Based on the work of ValentinChCloud Shiny GIE.
Using the docker rocker/shiny to install Shiny.
Adding Galaxy Connectors from erasche Docker RStudio Container to import/export datasets.
Using the Galaxy IE helpers by bgruening.

Galaxy Interactive Environment installation [toc]

If you have not already installed your Galaxy Interactive Environment, you can follow the tutorial at the following link : Tutorial for GIE installation

How to use this Docker image [toc]

From the pre-built image [toc]

FROM quay.io/workflow4metabolomics/gie-shiny:latest

Build the image locally [toc]

Build your own image

Docker is a pre-requirement for this project. You can build the container with:

$ docker build -t gie-shiny .

And run it

The build process can take some time, but if finished you can run your container with:

$ docker run -p 3838:3838 -v /home/user/foo/:/import/ -t gie-shiny

and you will have a running Shiny instance on http://localhost:3838/.

How to interact with Galaxy [toc]

Within the R application file, you can interact with your history files thanks to Galaxy Connectors. See the example below to import or export files :

gx_get(FILE_ID)
gx_get(FILE_ID1, FILE_ID2, ...)
gx_get(FILENAME, identifier_type = "name")
gx_get(FILENAME1, FILENAME2 , ... , identifier_type = "name")

gx_put(FILENAME)
gx_put(FILENAME1, FILENAME2, ...)

Application list [toc]

gie-shiny-chromato : This application allows to visualize TIC and BPC chromatograms.
gie-shiny-pca : This application allows to visualize PCA.

workflow4metabolomics/gie-shiny