Graded Assignment I: Markdown and Unix shell basics

Week 2 graded assignment – due Sunday Sep 7 at 11:59 pm

Author
Affiliation

Jelmer Poelstra

CFAES Bioinformatics Core, Ohio State University

Published

August 29, 2025

Modified

September 5, 2025

Overview

This graded assignment is worth 10 points and is due on Sunday Sep 7th. It consists of creating two Markdown files:

  1. One with notes and reflections on what you learned this week
  2. Another that includes Unix shell code.

This assignment revolves around the material for week 2; the skills you will practice are Markdown, VS Code, and Unix shell basics.

Directions and grading

Submission expectations

  • Deadline: Sunday Sep 7th at 11:59 pm.
  • Submission: You don’t need to submit anything or notify the instructors: we will simply look for these files in the appropriate location at OSC. (We will also be able to see when the files were last modified.)
  • When to start: We recommend that you only get started with this assignment after Thursday’s class.

Academic integrity

Use of generative AI Tools (e.g. ChatGPT, Microsoft Copilot, Google Gemini) is not permitted.
Getting help on the assignment is not permitted
Collaborating, or completing the assignment with others, is not permitted
Copying or reusing previous work is not permitted
Open-book research for the assignment is permitted
APA Citations and/or formatting for this assignment are not required

Rubric

Part A

Criterion Points
Markdown formatting 2.5
Class notes content 2.5

Part B

Criterion Points
Markdown formatting 1
8 numbered steps (0.5 pts each) 4

Detailed steps

General

  • You will be working on two Markdown files, which you should create and write in VS Code at OSC.
  • You should save both files with a .md extension, in a dir week02/GA1 within your personal dir at /fs/ess/PAS2880/users/<user>.

Specific requirements for the Markdown files — include each of the following components in at least one of your files:

  • Use several header levels and use them consistently
  • Include formatting like bold text, italic text, inline code, ordered/unordered lists, and hyperlinks
  • Complete Unix shell commands, like in Part II, should be in code blocks (not in inline code or as regular text)
  • Make sure you are not messing up whitespace – e.g. separate paragraphs appropriately.

Part A: A Markdown document with class notes

Write a summary of what you’ve learned so far in this course. The summary doesn’t need to be comprehensive, and can focus on elements that you think were interesting or that make sense to summarize.

The summary should be more wide-ranging than just hitting the below points, but make sure to highlight:

  • Things that you were excited to learn.

  • Things that you are (still) confused about.

  • You were given some recommendations this week, e.g. related to project file organization. Discuss at least one recommendation that you think will be really useful and one that you are not positive about (e.g. that you’re not sure you agree with or that you think would be problematic to implement in your projects in practice).

Part B: A Markdown document with Unix shell exercises

Copy each of the numbered instructions below into your document, and insert your answers in between. The Unix shell code that you came up with should be in Markdown code blocks, and the code output that you saw when your ran that code should also be part of your answer.

As an example, let’s say one of the assignment’s question was to print your current working directory – then the part of your document about that question could look like this:

1. Print your current working directory

```bash
pwd
```

The output of the command was: `/fs/ess/PAS2880/users/jelmer`.

It does not matter what your working dir is when you start this.

  1. Print the location of your Home directory to screen using a “path shortcut”. (Hint: you’ll need to preface the path shortcut with a command you learned.)

  2. Navigate to your Home directory using an “environment variable”.

  3. Would you say that you just moved to your Home dir using a relative path or using an absolute path? Why?

  4. Navigate from your Home dir to /fs/ess/PAS2880/users/$USER using a relative path. (Hint: This may be the most challenging question: Make sure to read the path shortcuts section and extrapolate from the examples there.)

  5. In the shell, type “ (one double-quote character) and press Enter. What is happening, why is that happening, and how can you get out of it? (Hint: read the section on keyboard shortcuts.)

  6. With the cal command, print a Julian calendar for three months using “long-form” (-- rather than -) options.

  7. Short-form options can be pasted together: e.g., -j -3 can be written as -j3. Do you think you can “paste together” long-form options as well? Test your intuition and report back.

  8. Are you currently located on a login node or a compute node at OSC? Why?

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