Environment Setup

Navigation

# Print current directory
pwd

# List files and directories
ls              # Basic listing
ls -l           # Detailed listing (permissions, size, date)
ls -la          # Include hidden files (starting with .)
ls -lh          # Human-readable file sizes

# Change directory
cd /path/to/dir     # Go to specific directory
cd ~                # Go to home directory
cd ..               # Go up one level
cd -                # Go to previous directory

File Operations

# Create files and directories
mkdir mydir             # Create directory
mkdir -p dir1/dir2      # Create nested directories
touch file.txt          # Create empty file

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

# Move/rename files
mv oldname.txt newname.txt      # Rename file
mv file.txt /path/to/dest/      # Move file

# Remove files
rm file.txt             # Delete file
rm -r mydir/            # Delete directory recursively
rm -i file.txt          # Ask before deleting

Viewing Files

# Display file contents
cat file.txt            # Show entire file
head file.txt           # Show first 10 lines
head -n 20 file.txt     # Show first 20 lines
tail file.txt           # Show last 10 lines
tail -f logfile.txt     # Follow file updates in real-time
less file.txt           # View with scrolling (q to quit)

# View compressed files
gzip -dc file.gz         # View gzipped file (works on macOS and Linux)
zless file.gz           # View gzipped file with scrolling

File Information

# Count lines, words, characters
wc file.txt             # Lines, words, characters
wc -l file.txt          # Lines only

# File size
du -h file.txt          # Size of file
du -sh mydir/           # Total size of directory

# Disk space
df -h                   # Disk usage summary

Searching

# Find files
find . -name "*.fastq"          # Find by name pattern
find . -type f -size +100M      # Find files larger than 100MB

# Search file contents
grep "pattern" file.txt         # Lines containing pattern
grep -r "pattern" mydir/        # Search recursively in directory
grep -i "pattern" file.txt      # Case-insensitive search
grep -c "pattern" file.txt      # Count matching lines

Pipes and Redirection

# Redirect output
command > file.txt      # Write output to file (overwrite)
command >> file.txt     # Append output to file
command 2> error.txt    # Redirect errors to file

# Pipes (send output to another command)
cat file.txt | head             # First 10 lines
cat file.txt | grep "pattern"   # Filter lines
cat file.txt | wc -l            # Count lines
cat file.txt | sort | uniq      # Sort and remove duplicates

Compression

# Gzip
gzip file.txt           # Compress (creates file.txt.gz)
gunzip file.txt.gz      # Decompress

# Tar archives
tar -cvf archive.tar dir/       # Create archive
tar -xvf archive.tar            # Extract archive
tar -czvf archive.tar.gz dir/   # Create compressed archive
tar -xzvf archive.tar.gz        # Extract compressed archive

Permissions

# View permissions
ls -l file.txt          # Shows -rw-r--r-- format

# Change permissions
chmod +x script.sh      # Make executable
chmod 755 script.sh     # rwx for owner, rx for others

# Change ownership
chown user:group file.txt

Process Management

# View running processes
ps                      # Your processes
ps aux                  # All processes
top                     # Interactive process viewer (q to quit)
htop                    # Better interactive viewer (if installed)

# Control processes
command &               # Run in background
Ctrl+C                  # Stop current process
Ctrl+Z                  # Suspend current process
bg                      # Resume suspended process in background
kill PID                # Terminate process by ID
killall processname     # Terminate by name

Useful Shortcuts

# Keyboard shortcuts
Ctrl+C          # Cancel current command
Ctrl+L          # Clear screen
Ctrl+A          # Move cursor to start of line
Ctrl+E          # Move cursor to end of line
Ctrl+R          # Search command history
Tab             # Auto-complete file/directory names
Up/Down         # Navigate command history

# History
history                 # Show command history
!123                    # Run command #123 from history
!!                      # Repeat last command