View markdown source on GitHub

Galaxy Interactive Tools



last_modification Last modification: Jun 14, 2022



@hexylena, @bgruening, and @jmchilton create Galaxy Interactive Environments (GIEs)

GIEs use Galaxy’s visualization framework to run certain types of interactive visualizations (e.g. Jupyter Notebook)

GIEs run in a docker container on the Galaxy server or a single remote Docker server

Speaker Notes



Support for Docker Swarm is added, allowing running a cluster for GIEs

Speaker Notes



@blankenberg creates Galaxy Interactive Tools (GxITs)

Building on the GIE concept, but run as tools

Tools run just as any other Galaxy job (e.g. via Slurm, HTCondor)

You will sometimes see Interactive Tools referred to as Interactive Environments version 2

Speaker Notes

Tool config syntax

<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="Interactive Jupyter Notebook" version="0.1">
        <container type="docker"></container>
        <entry_point name="Jupyter Interactive Tool" requires_domain="True">

Speaker Notes

Mapping clients to containers

Speaker Notes

Anatomy of a running Interactive Tool

Galaxy Interactive Tools Proxy Diagram

.reduce70[.footnote[The source for this figure can be found at:]]

Speaker Notes

Galaxy configuration

Enable docker on a destination in job_conf.xml and assign your GxITs to that destination

.left[Set in galaxy.yml:]

interactivetools_enable: true
interactivetools_map: /srv/galaxy/var/gie-proxy-sessions.sqlite

Speaker Notes

Proxy configuration

Use the proxy configuration that ships with Galaxy

Or the Node.js-based proxy

Speaker Notes


The default docker-enabled container exposes all datasets to the tool

Normally this isn’t bad (normal tools can’t be controlled by the user)

Interactive tools are fully user controllable

Solution: Embedded Pulsar

Speaker Notes

Embedded Pulsar

Runs a Pulsar server within the Galaxy application to “stage” (i.e. copy) inputs.

Speaker Notes

Thank you!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors! page logo This material is licensed under the Creative Commons Attribution 4.0 International License.