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Last pushed: 4 months ago
Short Description
Docker container for BATMAN package used for NMR data analysis
Full Description


This docker image provides an automated pipeline to infer the concentration of metabolites from 1D-NMR data. It's built upon a set of Python script for the pipeline, relying on BATMAN [1] for inference.

[1] Hao, Jie, et al. "BATMAN—an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model." Bioinformatics 28.15 (2012): 2088-2090

To build this image:

$ docker build -t joewandy/docker-batman .

To run the image, refer to In short:

docker run --rm -v ${NMR_DIR}:/home/rstudio/NMR --name docker-batman joewandy/docker-batman:latest

The analysis script, found at, will specifically look at /home/rstudio/NMR (in the container) to find all the input files it needs. In particular, put all your spectra (in Bruker format) in the 'spectra' folder of ${NMR_DIR}. The background signals should go into the 'background' folder in ${NMR_DIR}.

To start a bash shell in the container, run the script. You can access R-studio in the running container by going to http://localhost:8787/ in the browser and log in using the username 'rstudio' and password 'rstudio'. To access Jupyter notebook in the container, go to http://localhost:9999.

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