If you want to run the entire GTN material website locally or test your new training material you can do this!

Currently, the website is generated from the metadata and the tutorials using Jekyll, a simple static site builder. We can use Jekyll to run a server to check if the tutorial is correctly added and rendered.

Agenda

In this tutorial, you will learn how to run a local instance of the GTN website:

1. Installation of the requirements
2. Checking the website generation
3. Stopping the server
4. Conclusion

Installation of the requirements

The first step is to install the needed tools inside a conda environment. A conda environment is a directory that contains a specific collection of packages. For example here to run the website, we need ruby, pandas, requests, etc. By creating a conda environment and installing the needed tools there, we do not affect your main installation.

This step has to be done once.

We also need to make sure that a couple of other utilities and build requirements are present: git, curl & make. The easiest way to install these is with your package manager of choice - i.e. yum, apt, brew etc.

Hands-on: Install the requirements

1. Open a Terminal

2. Use your package manager to install git, curl and make

   • For Debian/Ubuntu: sudo apt update && sudo apt install git curl make
   • For Fedora/CentOs/RedHat: sudo yum install git curl make
3. (If not done yet) Clone the training material GitHub repository: git clone https://github.com/galaxyproject/training-material.git
4. Navigate to the training-material/ folder with cd

5. Set up the conda environment

   It will install some needed tools (ruby, nodejs, etc) in a protected environment, without interfering with the existing tools or versions.

   1. Install conda (if not already installed): make install-conda
   2. (You may need to exit the terminal and re-open for conda to be recognised. Navigate back to the same place.)
   3. Create the galaxy_training_material conda environment: make create-env
6. Install Jekyll and related modules into the conda environment: make install

Details: Troubleshooting `libxml2` errors

If you encounter an error about libxml2 on Linux, please try to install libxml2-dev (executing sudo apt install libxml2-dev) if on Debian/Ubuntu or libxml2-devel (executing sudo yum install libxml2-devel) if on Fedora/RedHat/CentOS, and re-run make install .

Checking the website generation

Once Jekyll and its modules are installed in our conda environment, we can check the generation of the website locally:

Hands-on: Checking the website generation locally

1. Run a local Jekyll server with make serve-quick
2. Visualize at http://localhost:4000/training-material/
3. Edit one of the tutorials:
   • For example, open topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.md in a text editor of your choice.
   • Make some changes to the Introduction paragraph, and save the file.
   • Refresh the tutorial page in your browser until you can see the changes you made.
     • this may take a little bit of time; in the terminal you can monitor when the regeneration is complete

With make serve-quick, a local Jekyll server will run in background. It will check the changes and regenerate the website accordingly. You may need to reload the page to see the changes (and sometimes to wait 1-2 minutes).

Tip

1. Use make serve instead of make serve-quick to get all plugins, but also configure the post, host and pass additional flags. This however can be quite slow.

2. Need to speed up the cloning step? You coud fetch only the latest commit of the main branch:

   $ git clone https://github.com/galaxyproject/training-material.git --depth 1 --branch main
   

3. Running on a VM or remote machine?

   If you are not running this on your local machine, but e.g. on a VM, you may need to configure a webserver to serve the website.

   Below is an example NGINX configuration (e.g. in /etc/nginx/sites-enabled/default)

   location /training-material/ {
     root /home/ubuntu/training-material/_site/;
   }
   

   Change the root path above to wherever you cloned the training material folder

Stopping the server

Once you are done, you can stop the server and clean your repository.

Hands-on: Stopping the server

1. Stop the server with CTRL-C
2. Clean the repository: make clean

Conclusion

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• Checking the generated website can be done locally

Frequently Asked Questions

Feedback

Did you use this material as an instructor? Feel free to give us feedback on how it went.
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Citing this Tutorial

1. Bérénice Batut, Björn Grüning, Saskia Hiltemann, Running the GTN website locally using the command line (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/contributing/tutorials/running-jekyll/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{contributing-running-jekyll,
author = "Bérénice Batut and Björn Grüning and Saskia Hiltemann",
	title = "Running the GTN website locally using the command line (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/contributing/tutorials/running-jekyll/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}
}

                   

Developing GTN training material

This tutorial is part of a series to develop GTN training material, feel free to also look at:

1. Contributing with GitHub via command-line
2. Overview of the Galaxy Training Material
3. Creating Interactive Galaxy Tours
4. Contributing with GitHub via its interface
5. Generating PDF artefacts of the website
6. Tools, Data, and Workflows for tutorials
7. Teaching Python
8. Running the GTN website online using GitHub CodeSpaces
9. Design and plan session, course, materials
10. GTN Metadata
11. Running the GTN website online using GitPod
12. Adding auto-generated video to your slides
13. Including a new topic
14. Adding Quizzes to your Tutorial
15. Principles of learning and how they apply to training and teaching
16. Updating diffs in admin training
17. Running the GTN website locally using the command line
18. Creating a new tutorial
19. Single Cell Publication - Data Plotting
20. FAIR Galaxy Training Material
21. Single Cell Publication - Data Analysis
22. Creating content in Markdown
23. Creating Slides
24. Updating tool versions in a tutorial

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/contributing/tutorials/running-jekyll/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: []

Feedback

5 stars	4
4 stars	1
2 stars	1
1 stars	1

June 2024

• 4 stars: Liked: Clear steps Disliked: A warning that the 'listen' gem will guide you to the local instance via 'http://0.0.0.0:4000/training-material/' which gives an 'unable to connect' screen. Even changing to 'httpS://...' does not work. Because of that, I spent a bit too much time debugging that while the link provided in the tutorial (http://localhost:4000/training-material/) does work.

October 2021

• 1 stars: Disliked: I have got the following error. The tutorial did not work for me. training-material$ make serve find: ‘_site/training-material’: No such file or directory find: ‘_site/training-material/*/*/slides/*’: No such file or directory find: ‘_site/training-material’: No such file or directory Tip: Want faster builds? Use 'serve-quick' in place of 'serve'. Tip: to serve in incremental mode (faster rebuilds), use the command: make serve FLAGS=--incremental mv: cannot stat 'Gemfile': No such file or directory mv: cannot stat 'Gemfile.lock': No such file or directory Configuration file: /home/alice/scchoi/downloads/training-material/_config.yml Dependency Error: Yikes! It looks like you don't have /home/alice/scchoi/downloads/training-material/_plugins/jekyll-environment_variables.rb or one of its dependencies installed. In order to use Jekyll as currently configured, you'll need to install this gem. If you've run Jekyll with `bundle exec`, ensure that you have included the /home/alice/scchoi/downloads/training-material/_plugins/jekyll-environment_variables.rb gem in your Gemfile as well. The full error message from Ruby is: 'cannot load such file -- bibtex' If you run into trouble, you can find helpful resources at https://jekyllrb.com/help/! ------------------------------------------------ Jekyll 4.2.1 Please append `--trace` to the `serve` command for any additional information or backtrace. ----------------------------

May 2021

• 5 stars: Liked: Everything :) Disliked: "topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.md" is no longer found, example can be changed to "topics/introduction/tutorials/r-basics/r_introduction.md" instead

June 2019

• 5 stars: Liked: Clearly explained. Disliked: In the first step (install requirements) - does there need to be an extra step before step 5, that says "conda activate galaxy_training_material" ?

February 2019

• 2 stars: Liked: Clear wording. Disliked: As a Windows user, I was not able to install requirements successfully.

October 2018

• 5 stars: Liked: Very very straightforward ! Disliked: Nothing...