Add CPT phage training material to Galaxy training (2nd try) by jasonjgill · Pull Request #6616 · galaxyproject/training-material

jasonjgill · 2026-01-25T04:16:51Z

Adds topics/phage-galaxy/ and one introduction tutorial.md with associated image files. I wasn't sure what other files (e.g., various .yaml files, the /docker/ directory) are strictly needed for function and which are just there as placeholders. I can add/edit these in as needed. The tutorials we have made are all just in .md format, we have not used the slide or other formats.

As requested in discussion with @shiltemann these changes were added to a clean fork of the training-material repo. The contributors.md will need to be updated separately.

…ge-galaxy/n.txt

shiltemann · 2026-01-28T10:46:40Z

@jasonjgill thanks a lot! No worries, I can take care of all the technical/infra stuff such as the yaml/docker files you mention.

I will also update the tutorial md files to GTN format and get back to you when I am done, then you can add some of the metadata such as learning objectives, and key points etc.

jasonjgill · 2026-03-10T18:41:24Z

@shiltemann is there anything I need to do on my end to get this merged?

shiltemann · 2026-03-11T14:24:43Z

@jasonjgill these tutorials are quite out of date with the latest GTN framework and need a bit of love. I plan to do that but just need to find the time. I am hoping next week that will be doable for me.

shiltemann · 2026-04-08T11:42:09Z

@jasonjgill would you be willing to invite me as a collaborator to the TAMU-CPT fork so that I can push changes directly to this PR?

shiltemann

Hi @jasonjgill I am just commenting here so you get a sense of improvements that need to be made, but I am happy to help make these changes for this tutorial.

In general, this tutorial is not quite as hands-on as usual in the GTN, it explains a lot of the Galaxy interface, but without explicit hands-on steps for the user to follow. Possible solutions could be:

Include one of the existing Galaxy introductions in your topic
Turn this into a slide deck rather than a hands-on tutorial
Update this tutorial to add hands-on boxes with explicit instruction to follow, and data in Zenodo etc.

As for the topic, does a new "virology" topic with a phage subtopic sounds ok to you? We have a few other virology tutorials in different topics that could find a nice home there. There are a few more additions needed to set up a proper GTN topic, but I can take care of those.

shiltemann · 2026-04-08T12:03:26Z

topics/phage-galaxy/introduction/tutorials/introduction-to-phage-galaxy/tutorial.md

+topic_name: introduction
+tutorial_name: introduction-to-cpt-galaxy
+---
+Last updated: Feb. 7 2024


this can be removed, we automatically add it to the tutorial overview box

shiltemann · 2026-04-08T12:04:24Z

topics/phage-galaxy/introduction/tutorials/introduction-to-phage-galaxy/tutorial.md

+topic_name: introduction
+tutorial_name: introduction-to-cpt-galaxy


these two metadata fields are not used, we can remove them.

We will, however, need some additional minimal metadata

layout: tutorial_hands_on title: Introduction to the Phage Galaxy level: Introductory zenodo_link: questions: - What is the Phage Galaxy? - add more questions objectives: - Add some objectives - What will they learn key_points: - take home message 1 - take home message 2 time_estimation: 1H contributions: authorship: - jasonjgill editing: - shiltemann

shiltemann · 2026-04-08T12:05:30Z

topics/phage-galaxy/introduction/tutorials/introduction-to-phage-galaxy/tutorial.md

+> ### Agenda
+>
+> In this tutorial, the following topics will be reviewed:
+> 
+> 1. First-time users
+>    > * Registering an account in Galaxy and Apollo
+> 2. Tools
+>    > * Uploading Data
+>    > * Choosing and Executing a Tool
+> 3. Histories
+>    > * The Current History
+>    > * History Information
+>    > * Datasets
+>    > * Managing Datasets Individually
+>    > * Switching Histories
+> 4. Workflows
+>    > * Importing a Workflow
+>    > * Running a Workflow
+>
+{: .agenda}


The agenda can be autogenerated from the section headings, so that we dont have to manually update it whenever we change the tutorial, we can add

> <agenda-title></agenda-title> > > In this tutorial, we will cover: > > 1. TOC > {:toc} > {: .agenda}

shiltemann · 2026-04-08T12:06:03Z

topics/phage-galaxy/introduction/tutorials/introduction-to-phage-galaxy/tutorial.md

+tutorial_name: introduction-to-cpt-galaxy
+---
+Last updated: Feb. 7 2024
+


please add a few sentences introduction about the tutorial above the Agenda, this will be used in e.g. social media link previews.

shiltemann · 2026-04-08T12:06:50Z

topics/phage-galaxy/introduction/tutorials/introduction-to-phage-galaxy/tutorial.md

+> ### {% icon tip %} Note that…
+> The screenshots displayed here may not precisely reflect what you see on your screen. As Galaxy is regularly updated, it is possible that the current tool or workflow version is different. Look for the most recent workflows/tools.
+{: .tip}


nowadays, the boxes are written a bit differently

Suggested change

> ### {% icon tip %} Note that…

> The screenshots displayed here may not precisely reflect what you see on your screen. As Galaxy is regularly updated, it is possible that the current tool or workflow version is different. Look for the most recent workflows/tools.

{: .tip}

> <tip-title> A note about screenshots </tip-title>

> The screenshots displayed here may not precisely reflect what you see on your screen. As Galaxy is regularly updated, it is possible that the current tool or workflow version is different. Look for the most recent workflows/tools.

{: .tip}

shiltemann · 2026-04-08T12:08:46Z

...ge-galaxy/introduction/images/introduction-to-cpt-galaxy-screenshots/10_expanded_dataset.png

all screenshots should be updated to a more recent version of Galaxy

shiltemann · 2026-04-08T12:15:02Z

topics/phage-galaxy/introduction/tutorials/introduction-to-phage-galaxy/tutorial.md

+> ### {% icon tip %} File Format Issues?
+> If Galaxy does not detect the file type properly, the user can set the file type. As this is a rare occurrence, be sure to double check the file is formatted properly before overriding Galaxy.
+{: .tip}


We have a large library of FAQs for common tasks like setting the file format.

You can use these like so:

{% snippet faqs/galaxy/datasets_change_datatype.md datatype="fasta" %}

shiltemann · 2026-04-08T12:15:34Z

topics/phage-galaxy/introduction/tutorials/introduction-to-phage-galaxy/tutorial.md

+> * [This tutorial](https://galaxyproject.github.io/training-material/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html) offers many different examples of various means of uploading data into Galaxy.
+{: .comment}
+
+Once the file has been detected by Galaxy, it will appear in the upload window.


all input datasets should be uploaded to Zenodo, and links provided here

shiltemann · 2026-04-08T12:15:57Z

topics/phage-galaxy/introduction/tutorials/introduction-to-phage-galaxy/tutorial.md

+
+Galaxy tools process input files and produce output files. To upload data from the user’s local device, click on the upload symbol in the top right-hand corner of the Tools column on the left side of the screen.
+
+![](../../images/introduction-to-cpt-galaxy-screenshots/2_upload_symbol2026.png)


all actions we want learners to perform, should be placed inside hands-on boxes

shiltemann · 2026-04-08T12:17:44Z

topics/phage-galaxy/introduction/tutorials/introduction-to-phage-galaxy/tutorial.md

+> * Translate said DNA sequences to protein sequences
+> * Run those protein sequences through BLASTp
+
+Doing these tasks one by one would mean keeping track of *at least* 4 files. The user would have to wait for one tool to finish before executing the next one. This is where workflows come in handy:


You can already start a tool before the previous one is finished in Galaxy

jasonjgill added 10 commits January 6, 2026 14:41

Create directory phage-galaxy

3f803af

Create folder

03abf4d

Add tutorial.md

5d07ee4

Create na.txt

bcc1bf8

Create na.txt

811a607

Delete topics/phage-galaxy/introduction/tutorials/introduction-to-pha…

ae75d48

…ge-galaxy/n.txt

Create na.txt

eef5c7e

Merge branch 'galaxyproject:main' into main

2a0ea0f

Adding 1 introduction tutorial.md and images to phage-galaxy section

e2c40e4

added placeholder files to directories

d579ad0

shiltemann self-assigned this Apr 8, 2026

shiltemann reviewed Apr 8, 2026

View reviewed changes

		topic_name: introduction
		tutorial_name: introduction-to-cpt-galaxy


		Galaxy tools process input files and produce output files. To upload data from the user’s local device, click on the upload symbol in the top right-hand corner of the Tools column on the left side of the screen.

		![](../../images/introduction-to-cpt-galaxy-screenshots/2_upload_symbol2026.png)

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jasonjgill commented Jan 25, 2026 •

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