/docker-qupath

Docker image for QuPath to be used as Galaxy IT

Primary LanguageDockerfileMIT LicenseMIT

European Galaxy server

Docker image for QuPath - constructed for the use as Galaxy IT

QuPath Bioimage Analysis is now available in Galaxy.

QuPath in Galaxy

Run the image

You can start the container outside of Galaxy with:

docker run -i -t --rm -v /path/to/infile.tiff:/opt/qupath/infile.tiff -p 8080:5800 quay.io/galaxy/qupath-headless:0.4.3 bash

Once you are in the container you can start the application with:

/init

Add extensions to the image

Adding extensions is as easy as downloading the JAR file and placing them in the appropriate directory.

Configuration

This image is based on top of the fantastic work of Jocelyn Le Sage base GUI image. Please consult the documentation of the upstream container.

Galaxy integration

Galaxy can run arbitrary Virtual Research Environments (VREs). In Galaxy terms, such VRE's are called "Interactive Tools", as they are using the same subsystem then normal Galaxy tools. The only requirement is that those tools needs to run in containers and expose a port(s) to which Galaxy can redirect users. The Docker image for QuPath you can find in this repository. The Galaxy tool defintion for the QuPath Interactive tool can be found here.