appsysbiohkijena/jipipe repository overview

This repository contains CLI versions of JIPipe, starting with version 4.0.0 where the CLI was introduced.

The latest tag always points to the latest version of JIPipe. Please note that starting with JIPipe 6.0.0, Java 21 is used.

To use the CLI for processing data, you will need to mount one or multiple volumes.

docker run --rm -v $(pwd):/data appsysbiohkijena/jipipe:latest run --project /data/project.jip --output-folder /data/output