Workflows are a powerful Galaxy feature that allows you to scale up your analysis by performing an end-to-end analysis with a single click of a button. In order to keep provenance of the workflow invocation (an invocation of a workflow means one run or execution of the workflow) it can be exported from Galaxy in the form of a Workflow Run Crate RO-Crate profile.

Agenda

In this tutorial, you will learn how to create a git repo, and begin working with it.

1. Enable RO-Crate on your local instance
2. Import an example workflow
3. Run the workflow
4. Export the Workflow Run Crate

Additionally, the exported Workflow Run Crate allows for sharing workflow run provenance with those unfamiliar with Galaxy and its standard export format.

This tutorial will guide you through the steps of defining such a report for your workflow, .

This tutorial will show you how to generate Galaxy-based Workflow Run RO-Crate after running the workflow.

Hands-on: Choose Your Own Tutorial

This is a "Choose Your Own Tutorial" section, where you can select between multiple paths. Click one of the buttons below to select how you want to follow the tutorial

Are you running Galaxy locally ?

Locally Not_locally

Import an example workflow

For this tutorial, we will use the workflow from the Galaxy 101 for everyone tutorial. If you have not done this tutorial yet, the only thing you need to know is that this is a workflow that takes as input a table of data about different species of iris plants, this table is subsequently sorted and filtered, and some plots are made. The specifics of the workflow are not important for this tutorial, only that it outputs a number of different kinds of outputs (images, tables, etc).

We will start by importing this workflow into your Galaxy account:

Hands-on: Import the workflow

1. Import the workflow into Galaxy

   Hands-on: Importing and launching a GTN workflow

   Launch Galaxy 101 for Everyone (View on GitHub, Download workflow) workflow.

   Click to Launch Galaxy 101 for Everyone (View on GitHub, Download workflow)

   Tip: If this does not work

   • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
   • Click on galaxy-upload Import at the top-right of the screen
   • Paste the following URL into the box labelled “Archived Workflow URL”: https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-reports/workflows/galaxy-101-everyone.ga
   • Click the Import workflow button

   Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Run the workflow

Galaxy will produce several export options for any workflow. The default export gives us a serialization of the invocation data model while the RO-Crate export gives an Workflow Run Crate which includes the default export as well.

Let’s run the workflow and export the RO-Crate.

Hands-on: Run the workflow

1. Import the file iris.csv via link

   https://zenodo.org/record/1319069/files/iris.csv
   

   Tip: Importing via links

   • Copy the link location

   • Click galaxy-upload Upload Data at the top of the tool panel

   • Select galaxy-wf-edit Paste/Fetch Data

   • Paste the link(s) into the text field

   • Press Start

   • Close the window

2. Run GTN Training: Galaxy 101 For Everyone workflow using the following parameters:
   • “Send results to a new history”: No
   • “1: Iris Dataset”“: the iris.csv file we just uploaded

   Tip: Running a workflow

   • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
   • Click on the workflow-run (Run workflow) button next to your workflow
   • Configure the workflow as needed
   • Click the Run Workflow button at the top-right of the screen
   • You may have to refresh your history to see the queued jobs

3. View the workflow outputs once the workflow has completed
   • The workflow produces several text and tabular outputs, and two plot (image) outputs

Export the Workflow Run Crate

After the workflow has completed, we can export the RO-Crate. The crate does not appear in your history, but can be accessed from the galaxy-history-options -> Show Invocations menu on the top right of your history OR on the left pannel from the galaxy-panelview Workflow Invocations .

Hands-on: Export the Workflow Run Crate

1. In the top right of your history, go to galaxy-history-options -> Show Invocations

   

2. Our latest workflow run should be listed at the top.
   • Click on it to expand it:

   

3. Click on the Export tab in the expanded view of the workflow invocation.

4. Click on the Export tab in the expanded view of the workflow invocation. You should see a page that contains three download options: - Research Object Crate (RO-Crate) - BioCompute Object - File

5. Click on the Generate galaxy-download option of the RO-Crate box (1st box)

   

Great work! You have created a Workflow Run Crate. This makes it easy to track the provenance of the executed workflow.

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• Galaxy Workflow Run Crates help you keep provenance of a workflow run / invocation.

• Galaxy Workflow Run Crates give extra context to the standard workflow run export

• Galaxy Workflow Run Crates can be exported from the top menu, User -> Workflow Invocations.

Frequently Asked Questions

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Citing this Tutorial

1. Paul De Geest, Exporting Workflow Run RO-Crates from Galaxy (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{fair-ro-crate-in-galaxy,
author = "Paul De Geest",
	title = "Exporting Workflow Run RO-Crates from Galaxy (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Funding

These individuals or organisations provided funding support for the development of this resource

BeYond-COVID

BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response. This project has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement № 101046203 (BY-COVID)

EuroScienceGateway

EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

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