Sometimes we want to share our workflows outside of Galaxy, like printing it on a poster. Making screenshots of Workflows looses a lot of detail, often to an degree where information is lost.

There are third party tools which can help us in making high resolution screenshots that preserve all details and produce pictures which are suitable for printing and sharing.

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

If you want to print your Galaxy Workflow on a poster, choose Print, otherwise Web is the better option.

Print Web

Agenda

In this tutorial we will cover:

1. Making a high-resolution Screenshot of a Galaxy Workflow
   1. Hiding the Galaxy UI
   2. Exporting high-res screenshots
2. Compressing Workflow Screenshots
   1. Palette Compression

Making a high-resolution Screenshot of a Galaxy Workflow

We will be using a feature built into the Firefox web browser to make screenshots larger than our screen. This only works in Firefox, so make sure you have it installed and are using it to follow the rest of this tutorial.

Hiding the Galaxy UI

We could cut it out of the final image using image-manipulation tools, but this is slow and cumbersome, especially for high-res images.

From Galaxy version 23.2 onwards there is a feature with which we can hide the Galaxy UI directly. It is meant to be used for embedding workflows, but can be accessed directly, which is perfect for purpose.

Hands-on: Hiding the Galaxy UI for a Workflow

1. Opening the Workflow Preview
   • Navigate to your Workflows list
   • Press “galaxy-eye View” on your desired Workflow
   • You should now see the preview page, which should look similar to this:

2. Add the following to the URL in your browser:

   &embed=true&buttons=false&about=false&heading=false&minimap=false&zoom_controls=false
   

3. You should now see your Workflow rendered as shown below:

   In this view, you can still zoom in and out using your mouse-wheel, and drag the canvas around.

Details: What does the text in the URL do?

These are so called query-parameters. They are chained to the existing parameters with a & symbol. Each parameter tells galaxy to render the UI slightly differently. If you’re curios at what they all do, try removing them individually and reloading the page.

Comment

If you cannot see a preview page like in the first screenshot, or if the query parameters have no effect, you are on a Galaxy version older than 23.2

You can still follow the rest of this tutorial to learn how to make high-resolution screenshots.

Exporting high-res screenshots

Now that we have a view of our Workflow without the Galaxy UI, let’s make a high-res screenshot using Firefox.

Tip: Can't fit your entire Workflow at once?

If you zoomed out as far as possible, but can’t view all of your Workflow, try the following:

• Navigate back to the full Workflow preview page (without the UI hidden)
• Click anywhere outside of the Workflow preview (e.g. on the about section)
• Zoom out the entire browser window a bit, by using Ctrl + Mouse Wheel, or Ctrl + -
• Re-add the query parameters we added in the previous section
• If you still can’t fit all of it, repeat the above steps

Hands-on: Creating a high-resolution screenshot

1. Open the Firefox Javascript console. To do this, either:
   • Use the shortcut Ctrl + Shift + K (On OS X Cmd + Shift + K)
   • Or navigate to the console using your mouse:
     • Menu
     • More Tools
     • Web Developer Tools
     • Console Tab

2. Resize or move the console

   The console may be in the way of your Workflow.

   You can make it take up less space by dragging down the bar at the top.

   You can also reposition it to the side, by selecting the three dots in the upper right corner of the console, and choosing a different position from: “Dock to Bottom”, “Dock to Right”, “Dock to Left”, “Separate Window”.

3. Make the screenshot

   In the Javascript console type:

   :screenshot --dpr 6
   

   After a short moment, a new screenshot should appear in your downloads folder.

   The value “6” after the --dpr option is just an example. Keep reading to learn how to choose the right dpr value.

Compressing Workflow Screenshots

In the following section, you will learn how to compress your screenshot to a smaller file-size.

Palette Compression

There are many ways to compress an image. Palette compression is particularly well suited for workflows. It can heavily reduce file size with minimal loss, if the amount of colors in an image is fairly low.

To compress our image, we will be using a piece of software called GraphicsMagick

This tool is known to be installed on usegalaxy.eu, we suggest you follow these steps there:

Hands-on: Uploading Your Image

1. Open usegalaxy.eu
2. At the top of the tool Tools panel (on the left), click galaxy-upload Upload Data
3. Select “Choose Local Files” from the bottom of the dialog
4. Select your saved screenshot, likely from your Downloads folder.
5. Click Start
6. Click Close

With the data on your Galaxy, we can start trying to compress it!

Hands-on: Compressing your screenshot

1. Run the Convert image format ( Galaxy version 1.3.40+galaxy0) tool
   • param-file “Image to convert”: screenshot.png
   • param-select “Reduce Color Palette”: Automatic
   • param-select “Output Format”: png

   This will have GraphicsMagick use automatic palette compression. This command may take a while.

2. Open the compressed image to check if everything is still clearly visible.

   Also check if the file size is now small enough for your purposes. (Click the dataset in your history to expand it to see the file size.)

3. If you want more control over your output file, you can provide a number of colours, instead of using the automatic reduction. Let’s re-run the tool and provide a number of colours you want to keep in your output image. This number should be in powers of two (4, 8, 16, 32, 64 etc.).

   Using smaller numbers will further reduce the file size at the cost of image quality. Smaller values do not always yield smaller files! Experiment a bit, or go with the option from step 4 for simplicity.

4. Run the Convert image format ( Galaxy version 1.3.40+galaxy0) tool
   • param-file “Image to convert”: screenshot.png
   • param-select “Reduce Color Palette”: Manual
   • param-select “Color Palette Size”: 4
   • param-select “Output Format”: png
5. Try different values until you get a result you like! Did you manage to create a smaller result than the automatic palette compression?

Tip: Tips for compressing images

1. JPEG is a naturally “lossy” format, you can try that instead of PNG
2. If the image is quite large, consider scaling it down with the “Resize %” parameter
3. Experiment with the colour palettes! You will likely be able to find one that is a good tradeoff between accuracy and file size for your use case.

Here’s an example workflow screenshot compressed from 2.4mb to 830kb. Click it to view it in full resolution.

You've Finished the Tutorial

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Key points

• Print ready screenshots

• Basic image compression

Frequently Asked Questions

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Citing this Tutorial

1. Laila Los, Creating high resolution images of Galaxy Workflows (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-posters/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{galaxy-interface-workflow-posters,
author = "Laila Los",
	title = "Creating high resolution images of Galaxy Workflows (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-posters/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}
}

                   

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/galaxy-interface/tutorials/workflow-posters/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:
- name: graphicsmagick_image_convert
  owner: bgruening
  revisions: 5376a7767fb3
  tool_panel_section_label: Convert Formats
  tool_shed_url: https://toolshed.g2.bx.psu.edu/

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