Best viewed in a Jupyter Notebook

This tutorial is best viewed in a Jupyter notebook! You can load this notebook one of the following ways

Launching the notebook in Jupyter in Galaxy

1. Instructions to Launch JupyterLab
2. Open a Terminal in JupyterLab with File -> New -> Terminal
3. Run wget https://training.galaxyproject.org/training-material/topics/data-science/tutorials/cli-bashcrawl/data-science-cli-bashcrawl.ipynb
4. Select the notebook that appears in the list of files on the left.

Downloading the notebook

1. Right click one of these links: Jupyter Notebook (With Solutions), Jupyter Notebook (Without Solutions)
2. Save Link As..

This is not a tutorial like most GTN content but a fun exercise for you to play around and learn a bit about the command line, and hopefully re-inforce the skills you covered in Basic and Advanced CLI skills.

Hands-on: Open a Jupyter Terminal

To best follow this tutorial, you should open a terminal.

Here are some instructions for how to do this on various environments.

Jupyter on UseGalaxy.* and MyBinder.org

1. Use the File → New → Terminal menu to launch a terminal.

   

2. Disable “Simple” mode in the bottom left hand corner, if it activated.

   

3. Drag one of the terminal or notebook tabs to the side to have the training materials and terminal side-by-side

   

CoCalc

1. Use the Split View functionality of cocalc to split your view into two portions.

   

2. Change the view of one panel to a terminal

   

Setup

git clone https://gitlab.com/slackermedia/bashcrawl
cd bashcrawl/entrance
# Run: cat scroll

Have fun, and good luck!

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• Learning linux can be fun!

Frequently Asked Questions

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Citing this Tutorial

1. Helena Rasche, CLI Educational Game - Bashcrawl (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/data-science/tutorials/cli-bashcrawl/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{data-science-cli-bashcrawl,
author = "Helena Rasche",
	title = "CLI Educational Game - Bashcrawl (Galaxy Training Materials)",
	year = "",
	month = "",
	day = ""
	url = "\url{https://training.galaxyproject.org/training-material/topics/data-science/tutorials/cli-bashcrawl/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} Computational Biology}
}

                   

Funding

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

Gallantries

This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.

Go Further

Do you want to extend your knowledge? Follow one of our recommended follow-up trainings:

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/data-science/tutorials/cli-bashcrawl/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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