CLI Educational Game - Bashcrawl

Authors:

Overview
Questions:

How can I move around on my computer?

How can I see what files and directories I have?

How can I specify the location of a file or directory on my computer?

How can I create, copy, and delete files and directories?

How can I edit files?

Objectives:

Explore the bash dungeon and fight monsters

Reinforce the learning of CLI basics such as how to change directories, move around, find things, and symlinkings

Requirements:

Foundations of Data Science

Hands-on: Hands-on: CLI basics: tutorial hands-on

Hands-on: Hands-on: Advanced CLI in Galaxy: tutorial hands-on

Time estimation: 2 hours

Level: Intermediate Intermediate

Supporting Materials:

Jupyter Notebook

FAQs

instances Available on these Galaxies

Possibly Working

UseGalaxy.eu

UseGalaxy.org

UseGalaxy.org.au

UseGalaxy.fr

Published: Sep 30, 2021

Last modification: Oct 23, 2023

License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License. The GTN Framework is licensed under MIT

purl PURL: https://gxy.io/GTN:T00075

version Revision: 9

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

Instructions to Launch JupyterLab

Open a Terminal in JupyterLab with File -> New -> Terminal

Run wget https://training.galaxyproject.org/training-material/topics/data-science/tutorials/cli-bashcrawl/data-science-cli-bashcrawl.ipynb

Select the notebook that appears in the list of files on the left.

Downloading the notebook

Right click one of these links: Jupyter Notebook (With Solutions), Jupyter Notebook (Without Solutions)

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

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

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

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

CoCalc

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

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!

Key points

Learning linux can be fun!

Frequently Asked Questions

Have questions about this tutorial? Check out the tutorial FAQ page or the FAQ page for the Foundations of Data Science topic to see if your question is listed there. If not, please ask your question on the GTN Gitter Channel or the Galaxy Help Forum

Feedback

Did you use this material as an instructor? Feel free to give us feedback on how it went.
Did you use this material as a learner or student? Click the form below to leave feedback.

Citing this Tutorial

Helena Rasche, gallantries, CLI Educational Game - Bashcrawl (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/data-science/tutorials/cli-bashcrawl/tutorial.html Online; accessed TODAY
Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

@misc{data-science-cli-bashcrawl,
author = "Helena Rasche and gallantries",
	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}
}

                   

Congratulations on successfully completing this tutorial!

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

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: []