Including a new topic

Author(s) orcid logoBérénice Batut avatar Bérénice Batut
Editor(s) orcid logoHelena Rasche avatar Helena Rasche
Reviewers Saskia Hiltemann avatarHelena Rasche avatarBérénice Batut avatarAnthony Bretaudeau avatarNicola Soranzo avatarBjörn Grüning avatarMartin Čech avatarGildas Le Corguillé avatarSimon Gladman avatarNiall Beard avatar
Overview
Creative Commons License: CC-BY Questions:

  • How to include a new topic?

  • What kinds of Topics are possible?

Objectives:

  • Create a new topic

  • Set up the metadata for a topic

Time estimation: 30 minutes
Supporting Materials:
Published: Jun 4, 2018
Last modification: Nov 8, 2024
License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License. The GTN Framework is licensed under MIT
PURL: https://gxy.io/GTN:T00056
Rating: 4.0 (1 recent ratings, 2 all time)
Revision: 31

Each training material is related to a topic. All training materials (slides, tutorials, …) related to a topic are found in a dedicated directory (e.g. transcriptomics directory contains the material related to exome sequencing analysis).

Directory structure

Each topic has the following structure:

├── README.md
├── metadata.yaml
├── images
├── docker
│   ├── Dockerfile
├── slides
│   ├── index.html
├── tutorials
│   ├── tutorial1
│   │   ├── tutorial.md
│   │   ├── slides.html
│   │   ├── data-library.yaml
│   │   ├── workflows
│   │   │   ├── index.md
│   │   │   ├── workflow.ga
│   │   ├── tours
│   │   │   ├── tour.yaml

images directory

The images directory collects all images/pictures needed for the training materials related to the topic, i.e pictures for the slides or the tutorials.

Images shared between several topics are in the shared/images directory at the root.

All images for the slides must be in images directory. The images must be in good quality. The sources (svg or other) of the images must also be added to the images directory. We encourage you to use yEd to easily generate diagrams and Inkscape for any other images.

tutorials directory

This directory collects the materials related to the topic, one material per subdirectory, though it may consist of slides, tutorials, or both.

The tutorials are hands-on built for workshop and self-training, with description of the whole infrastructure needed to run the tutorial on any Galaxy instance (tools, data library, etc).

The templates for the tutorials are different from the other pages to help users to focus on the content of the tutorial. To improve the output of the tutorial, several metadata are mandatory for every tutorials, such as the requirements or the objectives of the tutorials. Boxes are also used to highlight some key points as the hands-on or the tips.

The content of each tutorial is generated with Jekyll from a Markdown file and some metadata (e.g. the requirements, the Zenodo link, the questions) defined inside the metadata of the related topic.

Comment: Contributing

Want to contribute to a tutorial? Check out our training materials about that.

Sometimes, an hands-on tutorial is not the most appropriate format for a tutorial and slides are better.

docker directory

For each topic, a flavored Docker image must integrate the tools needed for the tutorials. The corresponding image must be based on official Galaxy Docker images.

The docker image will also integrate the Galaxy tours available for each topics and the workflows.

Agenda

In this tutorial, we will deal with:

  1. Directory structure
  2. Creating a new topic with it’s own materials
    1. Defining the topic
    2. Creating the skeleton for the topic
    3. Adapt the metadata for your topic
  3. Creating a tag based topic
    1. Defining the topic
    2. More manual tag based topics
  4. Conclusion

There are two kinds of topics we will cover: topics with their own materials, and synthetic topics that are based solely on a tag. For large collections of materials around a single central theme a topic with materials is a good choice. However, sometimes you will want to highlight materials spread across numerous or disparate topics like e.g. Cancer or SARS-CoV-2 tutorials where you might have individual tutorials on assembly or transcriptomics, but you’d like a single page listing all of them.

Creating a new topic with it’s own materials

Defining the topic

When we structured the repository, we decided to use as topics the categories that are used in the ToolShed. The ToolShed assigns a category to each tool. Therefore, to decide where to put your tutorial, have a look at which ToolShed’s category the main tools in your tutorial belong. For example, this tutorial will rely on the NCBI Blast+ tool.

Hands-on: Defining the topic for the tutorial
  1. Search for NCBI Blast+ on the ToolShed

  2. Check in which category it has been placed

    Question

    In which topic will you put the new tutorial?

    If we search for NCBI Blast+ in the ToolShed, it is placed in 2 categories (bottom): “Next Gen Mappers”, and “Sequence Analysis”. We decided to put it in “Sequence analysis” because this is the most general one for this tutorial.

In this tutorial, we want to add a new topic called about “my-favorite-topic”.

Creating the skeleton for the topic

Once the topic name has been chosen, we can create it.

Hands-on: Create all the required files and folders structures automatically
  1. Open a terminal

  2. Run (by adapting the information between the quotes)

    $ planemo training_init \
         --topic_name "my-favorite-topic" \
         --topic_title "Test" \
         --topic_target "use" \
         --topic_summary "Summary of the topic"
  3. Check that a new directory has been generated in topics
  4. Check that a YAML file with your topic name has been generated in metadata folder

  5. Make sure that Jekyll is running

    Comment: Jekyll

    Want to learn how to start Jekyll? Check out our tutorial to serve the website locally

  6. Check if the topic has been correctly added at http://localhost:4000/training-material/

Adapt the metadata for your topic

Several metadata are defined in metadata.yaml file in your topic folder to :

A dictionary/map

(Required) name
Free Text

The internal identifier for a topic, it should be the same as the folder name.

Example(s) 

name: epigenetics

name: sequence-analysis

name: admin

Required Pattern: Must match the following regular expression 

/^[a-z0-9_-]+$/

(Required) type
Free Text

The type of topic, some have subtly different behaviours.

admin-dev
should be used for admin and developer topics that are not scientifically focused.
basics
Only used for galaxy-interface type topics
data-science
Topics which are not necessarily Galaxy focused but expand into broader communities
use
These topics use galaxy for some analysis
instructors
Specific to topics related to instruction of Galaxy

Possible Values:

  • admin-dev
  • basics
  • data-science
  • use
  • instructors

Example(s) 

type: "admin-dev"

type: "basics"

type: "data-science"

type: "use"

type: "instructors"

(Required) title
Free Text

Title of the topic, this is displayed for users to see.

Example(s) 

title: Proteomics

title: Variant Analysis

(Required) summary
Free Text

A longer description of the contents of this topic

Example(s) 

summary: Statistical Analyses for omics data and machine learning using Galaxy tools

(Required) editorial_board
List of Items

List of Items

A dictionary/map

(Required) description
Free Text

Some text to go along with the call to action

(Required) link
Free Text

A link target (full qualified please)

(Required) link_text
Free Text

What goes on the button

Free Text

One of the icons from _config.yml

Free Text

Any custom CSS you might want to apply to a specific topic. This could be overriding e.g. the masthead colour (beware, will potentially conflict with themes.)

This is generally not a recommended property to set on topics, and something that is only used as part of outreach efforts to import content into the GTN.

Example(s) 

custom_css: - :root { --brand-color: red; }

Free Text

The image ID for an image which contains all of the tools and data for this topic.

Example(s) 

docker_image: quay.io/galaxy/sequence-analysis-training

Boolean

true to hide your tutorial from the topic page (optional). This is useful if you need a tutorial for a workshop, but have not finished making it up to GTN standards.

List of Items

Free Text

Link to a gitter channel that is more relevant for this topic than the default. E.g. a single cell topic, you could use Galaxy-Training-Network/galaxy-single-cell to link to their specific chat room in all of the child tutorials by default.

Example(s) 

gitter: Galaxy-Training-Network/galaxy-single-cell

gitter: galaxy-genome-annotation/Lobby

Free Text

The specific learning path you wish to reference as a call-to-action for views who aren’t sure where to get started.

It must be the name of a file in learning-pathways, without the .md suffix. This is not validated so, please make sure it’s correct :)

Example(s) 

learning_path_cta: intro-to-galaxy-and-genomics

learning_path_cta: admin-training

A dictionary/map

The specific learning path you wish to reference as a call-to-action for views who aren’t sure where to get started.

It must be the name of a file in learning-pathways, without the .md suffix. This is not validated so, please make sure it’s correct :)

Example(s)

For Beginners: intro_single_cell
For Intermediate Users: intermediate_single_cell
For Coding Enthusiasts: coding_single_cell

Any key permitted
Free Text

Free Text

A logo identifier (e.g. GTN) should be used by default, but may be swapped out for special logos from the assets folder.

Free Text

The alt text for the logo (MANDATORY).

Free Text

A custom image to show on the link preview in external applications (e.g. when the URL is pasted into Twitter)

Example(s) 

og_image: /assets/images/gat.png

Required Pattern: Must match the following regular expression 

/^\/.*/

List of Items

Example(s)

references:
- - |
    authors: "Vaudel M, et al."
    title: "Shedding light on black boxes in protein identification."
    link: "https://www.ncbi.nlm.nih.gov/pubmed/24678044"
    summary: "An extensive tutorial for peptide and protein identification, available at http://compomics.com/bioinformatics-for-proteomics. The material is completely based on freely available and open-source tools."

(Required) Sequence Value (List of items)
A dictionary/map

(Required) authors
Free Text

(Required) title
Free Text

(Required) link
Free Text

Free Text

List of Items

List of resources that the reader of the material should be familiar with before starting this training. The structure is identical to follow_up_training.

Example(s)

requirements:
- type: internal
  topic_name: statistics
  tutorials:
      - age-prediction-with-ml

(Required) Sequence Value (List of items)
A dictionary/map

(Required) type
Free Text

the type of link

Possible Values:

  • internal

Example(s) 

type: "internal"

Free Text

The name of the topic

List of Items

List of required tutorials inside that topic

List of Items

For large topics, we can define subtopics and create multiple tutorial lists, which separates the tutorials to help users find content that interests them more quickly.

A dictionary/map

(Required) id
Free Text

Subtopic ID, this should match what is used in tutorials.

Example(s) 

id: single-cell

Required Pattern: Must match the following regular expression 

/^[A-Za-z0-9_-]+$/

(Required) title
Free Text

Subtopic title, which is displayed for users to see.

Example(s) 

title: Maintaining a Production Galaxy

title: Single-cell RNA-seq

(Required) description
Free Text

A human readable textual description of a subtopic.

Example(s) 

description: - "Start here if you are new to RNA-Seq analysis in Galaxy"
- "These tutorials take you from raw sequencing reads to pathway analysis"
- "Tutorials about analysis of single-cell RNA-seq data"
- "Tutorials using a single published single-cell RNA-seq dataset for a variety of analyses"

Boolean

false to hide your topic from the production GTN. This is useful if you need a topic for a workshop, but have not finished making it up to GTN standards.

Boolean

If this is a tag based topic (no tutorials of it’s own) then you must set this flag to indicate it as such, otherwise you will find yourself with an empty topic page.

Boolean

For large topics with many subtopics, set this to true to generate a table of contents above the tutorial table to support quickly jumping to a subtopic.

Free Text

These are used to organise the home page tutorials only, not used anywhere else.

Possible Values:

  • technology
  • field

Example(s) 

topic_type: "technology"

topic_type: "field"

Hands-on: Update the new topic to the website
  1. Open the metadata.yaml file in your topic folder
  2. Fill the correct metadata of the topic

  3. Make sure that Jekyll is running

    Comment: Jekyll

    Want to learn how to start Jekyll? Check out our tutorial to serve the website locally

  4. Check how it changes the local website

Subtopics

For large topics, we can define subtopics and create multiple tutorial lists, within a topic’s metadata.yaml

name: transcriptomics
type: use
title: Transcriptomics
summary: Training material for all kinds of transcriptomics analysis.
docker_image: "quay.io/galaxy/transcriptomics-training"

[...]

subtopics:
- id: introduction
  title: "Introduction"
  description: "Start here if you are new to RNA-Seq analysis in Galaxy"
- id: end-to-end
  title: "End-to-End Analysis"
  description: "These tutorials take you from raw sequencing reads to pathway analysis"
- id: visualisation
  title: "Visualisation"
  description: "Tutorials covering data visualisation"

Each subtopic has:

  • an ID, used as a reference in the tutorial
  • a short descriptive title
  • a longer description discussion what is contained in that subtopic

Tutorials can be assigned to subtopics by adding e.g. subtopic: singlecell to the tutorial metadata. An example of this subtopic division can be found in the admin section

Creating a tag based topic

For tag based topics, first ensure that all of the relevant tutorials share a single tag, across all materials that should be included in this view.

Defining the topic

Compare with other topic level metadata files in the metadata/ directory of the training material. Then create a file of your own naming the topic and providing editorial board members and so on. We will use the Covid-19 synthetic topic as an example:

---
name: "covid19"
type: "use"
title: "SARS-CoV-2"
summary: "Tutorials covering analysis of SARS-CoV-2 (COVID 19)"
tag_based: true

editorial_board:
  - wm75

gitter: galaxyproject/sars-cov-2

As you can see it is very short, and there are only a handful of important points:

  • tag_based must be set to true
  • name must be equal to the tag name, that’s being used across tutorials.
  • subtopics must not be set.

With this done, all materials tagged covid19 will be aggregated and available under this synthetic topic. They are organised by the “parent” topic, so e.g. assembly tutorials are collected together and transcriptomics tutorials are also in a section together, similar to how other tutorials define subtopics.

More manual tag based topics

If you wish to more manually curate the tutorials listed in your tag-based topic, you can provide subtopics. These must have IDs that match tags that are expected to be found within your tag-based topic.

---
name: gmod
type: use
topic_type: technology
title: GMOD
edam_ontology: ["topic_0362"]

tag_based: true

subtopics:
  - id: jbrowse1
    title: "JBrowse 1"
    description: Learn to use JBrowse v1 here.
  - id: apollo2
    title: Apollo v2
    description: Apollo is a collaborative, real time genome annotation editor.

Here anything with a tag jbrowse1 will appear under the JBrowse section, same for apollo2 and the Apollo section. Tutorials may appear multiple times, but this is still useful as it gives you a way to provide additional organisation within your topic.

Conclusion

We just created a new topic. We can now fill it by creating new tutorials