lifs/jmztabm-cli repository overview

This project is the docker image providing the reference reader and validator implementation for mzTab for metabolomics 2.0+, based on the jmztab project at https://github.com/lifs-tools/jmzTab-m⁠.

Running the Docker Image

Please pull the Docker image of the validator cli:

docker pull lifs/jmztabm-cli

Then, run the following command, replacing VERSION with the current version, e.g. 1.0.4) and DATA_DIR with the local directory containing your mzTab-M files (examples at https://github.com/HUPO-PSI/mzTab/tree/master/examples/2_0-Metabolomics_Release⁠):

docker run -v YOUR_DATA_DIR:/home/data:rw lifs/jmztabm-cli:VERSION

This will invoke the default entrypoint of the container, which is a shell script wrapper calling the jmztab-m-cli Jar. It passes all arguments to the validator, so that all arguments that you would pass normally will work in the same way (please replace YOUR_MZTABM_FILE with the actual file’s name in YOUR_DATA_DIR:

docker run -v YOUR_DATA_DIR:/home/data:rw lifs/jmztabm-cli:VERSION -c YOUR_MZTABM_FILE

In order to list all possible command line arguments, run:

docker run -v YOUR_DATA_DIR:/home/data:rw lifs/jmztabm-cli:VERSION --help