ofilangi/docker-xcmsviewer

Dockerize xcmsViewer (R tool for LC-MS metabolomics). Create Dockerfile, install R dependencies, copy files, build image, run container, install xcmsViewer, and launch. Allows easy deployment and reproducibility.

docker-xcmsviewer

Build Image

docker build -t xcmsViewer .

Preprocessing Data

• Create extdata directory: mkdir extdata
• Put mzXML files into extdata
• Create a group file to assign group conditions

Example: extdata/group

23_0234.mzXML   A  
23_0245.mzXML   A

docker run -p 3838:3838 -v $(pwd)/extdata:/extdata -t xcmsViewer xcmsViewer_preprocess.R

Visualizing Data

docker run -p 3838:3838 -v $(pwd)/extdata:/extdata -t xcmsViewer xcmsViewer.R

Default values:

• PORT "3838"
• HOST "0.0.0.0"
• TRACE "FALSE"

Override env variables:

docker run --env TRACE="TRUE" -p 3838:3838 -v $(pwd)/extdata:/extdata -t xcmsViewer xcmsViewer.R