The dockerbuild file fot the tSPM+ R-package. The image is bases on rocker:rstudio. For a more detailed information regarding start options check the original documentation. There are two different versions of the docker container, a larger one containing the benchmark scripts and synthetic data, as well a lightweight one, which does not cointains then benchmark scripts and data. The benchmark scripts are in the folder /home/rstudio/benchmark and the sythnetic data for the benchmark is in the /home/rstudio/data directory. The two example uses cases provided in both variants are presented in the /home/rstudio/vignette folder.
Replace the tag with the current date or corresponding tag.
TAG=2023-09-05
docker build -t "ghcr.io/jonashuegel/tspmplusdocker:${TAG}" .
If you build it on your own make sure that the tag matches, when pulling from the Github container registry get the corresponding tag from the packages page. Then run the following command replacing everything in <> with your own values:
docker run -ti -e DISABLE_AUTH=true -e PASSWORD=<YOUR_PASS> -e RSTUDIO_WHICH_R=/usr/local/bin/R -p 127.0.0.1:8787:8787 -v .<path/to/data>:/home/rstudio/data -v <path/to/output>:/home/rstudio/output ghcr.io/jonashuegel/tspmplusdocker:${TAG}
Please cite our publication when using the package or docker container: Hügel, J., Sax, U., Murphy, S. N. & Estiri, H. tSPM+; a high-performance algorithm for mining transitive sequential patterns from clinical data. arXiv [cs.LG] (2023) doi:10.48550/arXiv.2309.05671