CLI Educational Game - Bashcrawl

Authors: orcid logoAvatarHelena Rasche AvatarErasmus+ Programme
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:
Time estimation: 2 hours
Level: Intermediate
Supporting Materials:
Last modification: Sep 28, 2022
License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License The GTN Framework is licensed under MIT
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.

    screenshot of jupyterlab showing the File menu expanded to show new and terminal option.

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

    screenshot of jupyterlab showing a toggle labelled simple.

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

    screenshot of jupyterlab with notebook and terminal side-by-side.

CoCalc

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

    screenshot of cocalc button to split views.

  2. Change the view of one panel to a terminal

    screenshot of cocalc swapping view port to that of 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

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Citing this Tutorial

  1. Helena Rasche, Erasmus+ Programme, 2022 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. 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 Erasmus+ Programme",
title = "CLI Educational Game - Bashcrawl (Galaxy Training Materials)",
year = "2022",
month = "09",
day = "28"
url = "\url{https://training.galaxyproject.org/training-material/topics/data-science/tutorials/cli-bashcrawl/tutorial.html}",
note = "[Online; accessed TODAY]"
}
@article{Batut_2018,
    doi = {10.1016/j.cels.2018.05.012},
    url = {https://doi.org/10.1016%2Fj.cels.2018.05.012},
    year = 2018,
    month = {jun},
    publisher = {Elsevier {BV}},
    volume = {6},
    number = {6},
    pages = {752--758.e1},
    author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{\i}}rez and Devon Ryan and Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Björn Grüning},
    title = {Community-Driven Data Analysis Training for Biology},
    journal = {Cell Systems}
}

Congratulations on successfully completing this tutorial!