CLI Introduction Exercises

These exercises accompany the Introduction to BASH module. They alternate between hands-on practice and knowledge checks.

---

Exercises developed by Kristine Lacek

Exercise 1 — Manual, Flags, and Arguments

View the full manual for each of these commands by running man <command>. Get quick help with the flags for each command by running <command> --help.

• ls
• sort
• head
• vim
• date
• time

Question:

Which of the commands listed above (ls, sort, head, vim, date, time) is a text editor?

Answer input

Attempt the answer; feedback will appear below.

vim is a powerful text editor available on virtually all Unix/Linux systems.

Question:

Which of the commands listed above does not have a manual entry (via man)?

Answer input

Attempt the answer; feedback will appear below.

time is typically a shell built-in (in bash/zsh), so it may not have a standalone man page. Use help time or type time instead.

---

Exercise 2 — Command Line Navigation

Complete the following steps in order:

1. Open your terminal.
2. Change directory to your home directory (~).
3. List the contents of that directory.
4. Make a directory within your home directory called 2026-BIFX-TRAINING.
5. cd to that new directory you just made.
6. Using .., cd back “up” to your home directory.
7. Try tab-complete: start the command cd 2026- then press Tab to complete the full directory name.
8. Try using your history: using only the up arrow to move through your recent commands, re-run the command you ran for step 2.

Question:

What command changes directory to your home directory?

Answer input

Attempt the answer; feedback will appear below.

cd ~, cd, or cd $HOME all navigate to your home directory.

Question:

What command creates a new directory called 2026-BIFX-TRAINING?

Answer input

Attempt the answer; feedback will appear below.

mkdir 2026-BIFX-TRAINING creates the directory in your current location.

---

Exercise 3 — Network and Downloads

Download the samplesheet from the workshop website for the next practical.

Linux/WSL (wget):

wget https://raw.githubusercontent.com/CDCgov/id-bioifx-workshop/refs/heads/main/practical/samplesheet.csv

macOS / Unix: macOS does not come with wget pre-installed, but you can install it with Homebrew. Homebrew is a package manager for macOS that simplifies the installation of software.

# Install Homebrew
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
# Install wget
brew install wget
wget https://raw.githubusercontent.com/CDCgov/id-bioifx-workshop/refs/heads/main/practical/samplesheet.csv > samplesheet.csv

---

Exercise 4 — File Viewing and Manipulation (Part 1)

1. Ensure your samplesheet.csv downloaded properly with cat.
2. Copy your samplesheet using cp to make samplesheet_copy.csv.
3. Rename your samplesheet_copy.csv to samplesheet2.csv using mv.
4. Using tail, output the last 20 lines of your samplesheet, and using redirect (>), write them to another file called samplesheet_subset.csv.
5. Using head and then piping into tail, output only the 8th line of samplesheet.csv.
6. Sort the samplesheet according to sample ID, numerically, then redirect to a file called samplesheet_sorted.csv.

Question:

What command outputs the last 20 lines of samplesheet.csv and writes them to samplesheet_subset.csv?

Answer input

Attempt the answer; feedback will appear below.

tail -n 20 (or tail -20) outputs the last 20 lines. The > operator redirects output to a file.

Question:

What command using head piped into tail outputs only the 8th line of samplesheet.csv?

Answer input

Attempt the answer; feedback will appear below.

head -8 gets lines 1–8, then tail -1 extracts just the 8th line.

Question:

What command sorts samplesheet.csv numerically and redirects to samplesheet_sorted.csv?

Answer input

Attempt the answer; feedback will appear below.

sort -n sorts numerically rather than alphabetically.

---

Exercise 5 — File Viewing and Manipulation (Part 2)

1. cat samplesheet_sorted.csv to append to samplesheet2.csv. Cat samplesheet2.csv — it should look twice as long!
2. cat samplesheet_sorted.csv to overwrite samplesheet2.csv. Cat samplesheet2.csv — it should look just like samplesheet_sorted.csv.
3. Rename samplesheet2.csv back to samplesheet_copy.csv.
4. Using rm and glob (*) remove both samplesheet_copy.csv and samplesheet_sorted.csv without removing samplesheet.csv.

Question:

What operator appends output to an existing file (without overwriting)?

Answer input

Attempt the answer; feedback will appear below.

>> appends to a file, while > overwrites it.

Question:

What operator overwrites a file with new output?

Answer input

Attempt the answer; feedback will appear below.

> redirects output and overwrites the target file.

Question:

What command removes samplesheet_copy.csv and samplesheet_sorted.csv using a glob, without removing samplesheet.csv?

Answer input

Attempt the answer; feedback will appear below.

rm samplesheet_*.csv matches files starting with samplesheet_ but not samplesheet.csv (which has no underscore).

---

Exercise 6 — Searching and Text Processing (Part 1)

1. Using wc on samplesheet.csv, how many lines are there?
2. Using wc on samplesheet.csv, how many characters are there?
3. Using cut on samplesheet.csv, output only the Barcode # field.
4. Make a file called sample_list.txt by cutting and redirecting unique sample IDs from your fastqs.
5. Bonus: Using tr and sort on samplesheet.csv, output the highest barcode number only (no “barcode”).

Question:

What command counts only the number of lines in samplesheet.csv?

Answer input

Attempt the answer; feedback will appear below.

wc -l counts lines in a file.

Question:

What command counts the number of characters in samplesheet.csv?

Answer input

Attempt the answer; feedback will appear below.

wc -m counts characters and wc -c counts bytes. For ASCII files they give the same result.

---

Exercise 7 — Searching and Text Processing (Part 2)

Download the influenza FASTA file:

wget https://raw.githubusercontent.com/CDCgov/id-bioifx-workshop/refs/heads/main/practical/influenza.fasta

1. Using grep with a flag or piping into wc, how many times does the sequence GGGGCGGGG (4G 1C 4G) appear in your influenza.fasta?
2. Using grep with the -A flag (--help if you don’t recall what that does), output all the A_HA_H1 sequences to a file called H1_HA.fasta.

Question:

What command counts how many times GGGGCGGGG appears in influenza.fasta?

Answer input

Attempt the answer; feedback will appear below.

grep -c returns the count of matching lines. Alternatively, pipe grep output into wc -l.

---

Exercise 8 — Searching and Text Processing (Part 3): sed

Now we will use sed to turn our H1_HA.fasta headers into strain names:

sed -s "s/find/replace/g"

Goal: >3004125441_N8KIRZTI_v1 | A_HA_H1 → >A/Country/3004125441_N8KIRZTI_v1/2026

Complete the following parts:

1. Part 1: Use sed -s to remove the lines with two dashes (--) from grep output, redirect to H1_HA_1.fasta.
   • Find: -- → Replace: nothing
2. Part 2: Use sed -s to replace > with >A/Country/ in H1_HA_1.fasta, redirect to H1_HA_2.fasta.
   • Since the replacement contains /, you will need to use another delimiter character (%, #) for your sed.

3. Part 3: Use sed -s to replace `

   A_HA_H1 with /2026 in H1_HA_2.fasta, redirect to H1_HA_3.fasta`.

   • Again, use an alternative delimiter since the replacement contains /.
4. Part 4: Rename H1_HA_3.fasta to H1_HA_final.fasta.

Intermediate challenge: Can you do this all in one command using multiple sed commands with pipe |?

Question:

When your find or replace string contains /, what alternative delimiter characters can you use with sed?

Answer input

Attempt the answer; feedback will appear below.

You can use any character as a sed delimiter. Common alternatives to / include %, #, |, and @.

---

Exercise 9 — Compression and Archives

Download, uncompress, and re-compress the following files:

• wget https://raw.githubusercontent.com/CDCgov/id-bioifx-workshop/refs/heads/main/practical/2012704893_273083_v1_H3_PCR_original_R1_001.fastq.gz
  wget https://raw.githubusercontent.com/CDCgov/id-bioifx-workshop/refs/heads/main/practical/2012704893_273083_v1_H3_PCR_original_R2_001.fastq.gz
  

Use ls -lah (the -h flag makes file sizes human-readable) to display the file sizes before and after compression.

Question:

What command uncompresses a .gz file?

Answer input

Attempt the answer; feedback will appear below.

gunzip (or gzip -d) decompresses .gz files.

Question:

What command compresses a file with gzip?

Answer input

Attempt the answer; feedback will appear below.

gzip <filename> compresses the file and adds the .gz extension.

---

Exercise 10 — Permissions and Ownership

1. Using wget, pull down permissions.txt at:
   https://raw.githubusercontent.com/CDCgov/id-bioifx-workshop/refs/heads/main/practical/permissions.txt
2. cat permissions.txt.
3. Using chmod, remove read permissions for owner on permissions.txt.
4. cat permissions.txt — what does it say now?
5. Using chmod again, add read permissions back to permissions.txt.
6. Using the up arrow to load your last wget command, pull down permissions.sh by changing the command’s final .txt to .sh.

Question:

What chmod command removes read permission for the owner on permissions.txt?

Answer input

Attempt the answer; feedback will appear below.

chmod u-r removes the read (r) permission for the user/owner (u).

Question:

What chmod command adds read permission back for the owner on permissions.txt?

Answer input

Attempt the answer; feedback will appear below.

chmod u+r adds the read (r) permission for the user/owner (u).