Module 2: The Basics

The reference module: the commands you will use 90% of the time. The goal is to build muscle memory so the terminal feels like a natural extension of your thought process, rather than a barrier to your research.

2.1 Navigation

Linux uses a hierarchical tree structure starting at the root (/).

# Print working directory — where am I?
pwd

# List files
ls            # basic listing
ls -l         # long format (permissions, size, date)
ls -la        # include hidden files (dotfiles like .bashrc)
ls -lh        # human-readable file sizes (KB, MB, GB)

# Change directory
cd /path/to/dir     # absolute path
cd relative/path    # relative path
cd ~                # home directory
cd ..               # parent directory
cd -                # previous directory (toggle)
                    # Note: extremely useful when jumping between
                    # a data directory and a script directory

2.2 File Operations

Creating, Copying, Moving, Renaming

# Create
touch file.txt          # create empty file (or update timestamp)
mkdir mydir             # create directory
mkdir -p a/b/c          # create nested directories (parent/child/grandchild)

# Copy
cp file.txt backup.txt          # copy file
cp -r mydir/ mydir_backup/      # copy directory recursively

# Move / Rename
mv file.txt newname.txt         # rename
mv file.txt /other/path/        # move

Deleting

There is no trash can in the terminal. Deletion is permanent.

rm file.txt             # delete file
rm -r mydir/            # delete directory recursively
rm -ri mydir/           # interactive — asks before every file

Wildcards (Globbing)

* matches anything (e.g., *.csv matches all CSV files)
? matches exactly one character (e.g., file?.txt matches file1.txt but not file10.txt)

2.3 Viewing & Searching

Viewing Files

# View entire file
cat file.txt            # dump whole file to terminal (bad for large files)
less file.txt           # paginated view (q to quit, / to search)

# View parts
head file.txt           # first 10 lines
head -n 20 file.txt     # first 20 lines
tail file.txt           # last 10 lines
tail -f logfile.log     # follow a log file in real-time

grep — The Search Tool

grep filters input line-by-line. Essential for bioinformatics (finding specific sequences, counting FASTA records, etc.).

# Basic search
grep "pattern" file.txt

# Case-insensitive
grep -i "pattern" file.txt

# Show line numbers
grep -n "pattern" file.txt

# Recursive search (all files in current directory)
grep -r "TODO" .

# Invert match (lines that do NOT match)
grep -v "error" log.txt

# Count matching lines
grep -c ">" sequences.fasta

2.4 Permissions

Every file has a mode string (e.g., -rwxr-xr--) defining who can do what.

The Bits

Symbol	Meaning	Octal Value
`r`	Read	4
`w`	Write	2
`x`	Execute	1

Changing Permissions (`chmod`)

# Symbolic mode (easier to read)
chmod +x script.sh        # add execute for everyone
chmod u+w file.txt        # add write for owner (u=user)
chmod go-r private.key    # remove read for group and others

# Numeric mode (faster to type)
chmod 755 script.sh       # rwx (7) for owner, r-x (5) for group/others
chmod 644 file.txt        # rw- (6) for owner, r-- (4) for group/others
chmod 600 private.key     # rw- (6) for owner, --- (0) for group/others

2.5 Pipes & Redirection

Redirection

Operator	Behavior
`>`	Overwrite output to a file
`>>`	Append output to the end of a file
`2>`	Redirect stderr (errors) only

echo "Analysis Complete" > status.txt    # creates/overwrites file
echo "Error found" >> log.txt            # appends to file

Pipes (`|`)

Passes the stdout of the left command to the stdin of the right command.

# Count number of Python files
find . -name "*.py" | wc -l

# Check for errors in the last 50 lines of a log
tail -n 50 app.log | grep "Error"

# Unique sorted values (classic combo)
cat data.txt | sort | uniq
# This is the Unix philosophy in action — small tools chaining
# together to solve complex problems without a custom script.