Docker container for Bruker TopSpin

TopSpin is the Bruker software suite for NMR data analysis. This repository does not contain any Bruker licensed software, instead we are providing an example how to install TopSpin into a software container.

Preface

This repository contains information to install the Linux version of TopSpin into a CentOS 7.x container. We used information from:

Following

• https://www.bruker.com/protected/en/services/user-manuals/nmr/installation.html (TopSpin 4.0 Installation Guide, Section 2.7)
• https://cdn.dal.ca/content/dam/dalhousie/pdf/Diff/nmr3/NMR%20Software/install_ts4.pdf
• https://repo-bbio.bruker.com/CentOS/7/TopSpinInstallationRequirements.html

To use the resulting installation, please

1. Obtain a valid license. Academic customers can get a free license, e.g. by going to https://www.bruker.com/protected/en/services/software-downloads/nmr/nmr-topspin-license-for-academia.html
2. Obtain the software installation file from https://www.bruker.com/protected/en/services/software-downloads/nmr/linux/linux-topspin.html (Section Current Releases with TopSpin 4.x.y & CMC-assist) e.g. the topspin-4.1.1.2-linux.sh from Bruker and place it into the directory where the Dockerfile resides.

Building

The base container can be built with

docker build -t nfdi4chem/topspin:latest .
docker tag nfdi4chem/topspin:latest nfdi4chem/topspin:4.1.1.2-0.3

Tagging with a specific version is recommended.

Running

docker run -v $PWD/testdata:/data --rm -it nfdi4chem/topspin:4.1.1.2-0.3 /data/ADG10003u_023 /data/out.jdx

The included test data ADG10003u_023 is a urine sample in the metabolomics study "MTBLS1: A metabolomic study of urinary changes in type 2 diabetes in human compared to the control group" https://www.ebi.ac.uk/metabolights/MTBLS1/.