Linux

Created

October 9, 2022

Modified

December 11, 2025

UNIX Shell Basics

## Basic command
pwd # Show current directory
cd /path/to/directory # Change directory
cd .. # Go up one level
cd - # Go to previous directory
cd ~ # Go to home directory
ls # List files and folders
ls -lhrt # List files with details, human-readable sizes, sorted by time, reverse order
mkdir folder_name # Create a new folder
mkdir -p /path/to/folder # Create nested folders
mv old_name new_name # Rename or move file/folder
rm file_name # Remove file
rm -r folder_name # Remove folder recursively
rm -f file_name # Force remove file without prompt
rm -rf folder_name # Force remove folder recursively without prompt
cp source_file destination_file # Copy file
cp -a /source/folder /destination/folder # Copy folder recursively with attributes
scp user@remote:/path/to/remote/file /local/destination/ # Copy file from remote server
scp /local/file user@remote:/path/to/remote/destination/ # Copy file to remote server
cat file_name # Display file content
zcat file_name.gz # Display compressed file content
less file_name # View file content with pagination
zless file_name.gz # View compressed file content with pagination
head -n 10 file_name # Show first 10 lines of a file
tail -n 10 file_name # Show last 10 lines of a file
wc -l file_name # Count number of lines in a file
history # Show command history
top # Display running processes
htop # Interactive process viewer (may need installation)
chmod 755 file_name # Change file permissions
chmod +x file_name # Make file executable
chown user:group file_name # Change file owner and group
tar xzvf archive.tar.gz # Extract tar.gz archive
tar czvf archive.tar.gz /path/to/folder # Create tar.gz archive
tar xjvf archive.tar.bz2 # Extract tar.bz2 archive
tar cjvf archive.tar.bz2 /path/to/folder # Create tar.bz2 archive
unzip archive.zip # Extract zip archive
zip -r archive.zip /path/to/folder # Create zip archive
ping google.com # Check network connectivity
ifconfig # Show network interfaces (may need installation)
ip addr show # Show network interfaces (modern alternative to ifconfig)
wget http://example.com/file # Download file from the internet
curl -O http://example.com/file # Download file using curl
## Intermediate command
grep "pattern" file_name # Search for a pattern in a file
grep -r "pattern" /path/to/directory # Recursively search for a pattern in a directory
sort file_name # Sort lines in a file
sort -u file_name # Sort and remove duplicate lines
uniq file_name # Remove duplicate lines (requires sorted input)
find /path/to/search -name "pattern" # Find files/folders by name
find /path/to/search -type f -size +100M # Find files larger than 100MB
cut -f1,3 file_name # Extract specific columns from a file (tab-delimited)
awk '{print $1, $3}' file_name # Extract specific columns using awk
sed 's/old/new/g' file_name # Replace text in a file
diff file1 file2 # Compare two files line by line
diff -r dir1 dir2 # Compare two directories recursively
ln -s /path/to/target /path/to/symlink # Create a symbolic link
tree /path/to/directory # Display directory structure as a tree (may need installation)
tree -L 2 /path/to/directory # Display directory structure up to level 2
du -h /path/to/directory # Show disk usage of a directory
du -sh /path/to/directory # Show total disk usage of a directory
du -h --max-depth=1 /path/to/directory | sort -h # Show disk usage of subdirectories sorted by size
rsync -av /source/folder/ /destination/folder/ # Sync folders
rsync -auzP /source/folder/ user@remote:/destination/folder/ # Sync to remote server with compression and progress
## Advanced command
| # Pipe output of one command to another
awk '{sum += $1} END {print sum}' file_name # Sum values in the first column
sed -n '2,5p' file_name # Print lines 2 to 5 of a file
xargs -n 1 rm < file_list.txt # Remove files listed in a file
## Show current shell
echo $SHELL

## Change default shell to bash
chsh -s /bin/bash
chsh -s /bin/zsh

File Compression

  • Commone tar flags:
    • -x = extract
    • -f = file
    • -v = verbose
    • -z = gzip compression
    • -j = bzip2 compression
    • -J = xz compression
    • -c = change to directory
    • -C = specify directory
    • -p = preserve permissions
    • --strip-components=N = remove N leading path components
    • --no-same-owner = do not preserve ownership
    • --no-same-permissions = do not preserve permissions
    • --wildcards = enable wildcard matching
    • --exclude='pattern' = exclude files matching pattern
    • --include='pattern' = include only files matching pattern
    • --transform='s/old/new/' = rename files during extraction
    • --skip-old-files = skip files that already exist
    • --overwrite = overwrite existing files
    • --keep-newer-files = keep files that are newer than the archive
    • --no-overwrite-dir = do not overwrite existing directories
    • --no-clobber = do not overwrite existing files
    • --remove-files = remove files after adding them to the archive
    • --no-recursion = do not recurse into directories
    • --no-auto-compress = do not automatically detect compression
    • --no-check-device = do not check device numbers when extracting
    • --no-same-time = do not preserve modification times
    • --no-same-permissions = do not preserve permissions
    • --no-same-owner = do not preserve ownership
    • --no-same-time = do not preserve modification times
## Extract .tar.gz file
tar -xf fuke.tar
tar -xzvf file.tar.gz
tar -xzf file.tgz

## Extract .tar.bz2 file
tar -xjf file.tar.bz2

## Extract .tar.xz file
tar -xJf file.tar.xz

## Extract to specific directory
tar -xzf file.tar.gz -C /path/to/directory

## List contents without extracting
tar -tzf file.tar.gz
tar -tf file.tar
## Extract zip files
unzip file.zip
unzip file.zip -d /path/to/directory

## List contents without extracting
unzip -l file.zip

## Extract .gz file
gunzip file.gz
gunzip -dk file.gz  # keep original file

## Extract .bz2 file
bunzip2 file.bz2

## Extract .xz file
unxz file.xz

## Extract .7z file
7z x file.7z

## Extract .rar file
unrar x file.rar
  • Common tar flags for compression
    • -c = create archive
    • -f = file name
    • -z = gzip compression (.tar.gz)
    • -j = bzip2 compression (.tar.bz2)
    • -J = xz compression (.tar.xz)
    • -v = verbose output
tar -cf archive.tar file1 file2 directory/

## gzip compressed
tar -czf archive.tar.gz file1 file2 directory/

## bzip2 compressed
tar -cjf archive.tar.bz2 file1 file2 directory/

## .tar.xz compressed
tar -cJf archive.tar.xz file1 file2 directory/

Shortcut

NoteAbout Terminal Shortcuts

These shortcuts work in most Unix-like terminals including Terminal.app on macOS, GNOME Terminal, and Windows Terminal with WSL.

Cursor Movement

Action Shortcut
Move to the beginning of line Ctrl + A
Move to the end of line Ctrl + E
Move one word backward Opt + ←
Move one word forward Opt + →
Move one character backward ←
Move one character forward →
Jump to the start of buffer Alt + <
Jump to the end of buffer Alt + >

Text Editing

Text Editing Shortcut
Delete the current line Ctrl + U
Delete to end of the line Ctrl + K
Clear the screen Ctrl + L
Delete one word backward Ctrl + W
Delete one character forward Ctrl + D
Delete one character forward Fn + Backspace
Delete one character backward Backspace
Delete from cursor to start Alt + Backspace
Delete from cursor to word end Alt + D

Process Management

Process Management Shortcut
Terminate a process Ctrl + C
Suspend a process Ctrl + Z
Exit the shell Ctrl + D
Send process to background Ctrl + Z then bg
Bring background process to fg fg

History & Commands

History & Commands Shortcut
Undo the last change Ctrl + _
Recall previous command ↑
Recall next command ↓
Search command history Ctrl + R
Exit history search Ctrl + G
Show history history
Run the last command !!
Run last pw command !pw
Run command # from history !<number>

Auto-Completion & Misc

Auto-Completion & Misc Shortcut
Auto-complete command TAB
List matching commands TAB TAB
Cycle through matches TAB TAB TAB...
Open last edited command Ctrl + X Ctrl + E
Transpose two characters Ctrl + T
Capitalize word at cursor Alt + C
Convert word to lowercase Alt + L
Convert word to uppercase Alt + U
Swap position with prev word Ctrl + W Alt + T

Permissions

Only the user can copy, execute, and change

chmod 700 /path/to/folder

700 means:

  • Owner: 7 (read = 4, write = 2, execute = 1; 4+2+1 = 7)
  • Group: 0 (no permissions)
  • Others: 0 (no permissions)

All can read and execute, only the owner can change

chmod 755 /path/to/folder
  • Owner: 7 (read = 4, write = 2, execute = 1; 4+2+1 = 7)
  • Group: 5 (read = 4, execute = 1; 4+1 = 5)
  • Others: 5 (read = 4, execute = 1; 4+1 = 5)

Give a user named someuser read, write, and execute permissions on the /path/to/folder directory

setfacl -m u:someuser:rwx /path/to/folder

Verify the Permissions

getfacl /path/to/folder

Remove all ACL entries for a user

setfacl -x u:someuser /path/to/folder

Change owner

sudo chown username:groupname /path/to/folder

Data transfer

  • Transfering data efficiently between local and remote systems:
    • wget: Download files directly from the internet to your local machine or server.
    • scp: Securely copy files between local and remote systems over SSH.
    • rsync: Synchronize files and directories efficiently, with options for selective copying and deletion.
## Basic command
rsync -av /source/folder/ /destination/folder/

## Sync source to destination
rsync -av --delete /source/folder/ /destination/folder/

## If you need two-way sync, run both directions
rsync -av --delete /folder1/ /folder2/
rsync -av --delete /folder2/ /folder1/

## Network sync
rsync -av --delete /local/folder/ user@remote:/remote/folder/

## Copy only new files (files that don't exist in the destination)
rsync -av --ignore-existing /source/folder/ /destination/folder/

## Copy only if source is newer
rsync -av --update /source/folder/ /destination/folder/
Note
  • --archive: Preserves permissions, timestamps, symbolic links, etc.
  • --verbose: Shows progress
  • --delete: Removes files in destination that don’t exist in source
  • --dry-run: Preview changes without actually syncing
  • --update: Only copy newer file
  • --ignore-existing: Skips files that already exist in destination (regardless of age)
  • --update: Only copies if source file is newer than destination
  • --no-perms: Don’t preserve Unix permissions
  • --no-times: Don’t preserve modification times
  • --inplace: Write directly without temp files
  • Sync remote server folders to local using rsync
## Remote server details
remote_user="username"
remote_host="hpcio2" # hpc2021-io1.hku.hk,hpc2021-io2.hku.hk  

## Define folders to sync (absolute paths)
## Format: "local_absolute_path:remote_absolute_path"
folders_to_sync=(
    # "/mnt/m/Reference:/lustre1/g/path_my/Reference"
    # "/mnt/m/WES/DFSP/Annovar:/lustre1/g/path_my/pipeline/somatic_variants_calling/data/DFSP/Annovar"
    "/mnt/m/WES/SARC/BAM:/lustre1/g/path_my/pipeline/somatic_variants_calling/data/SARC/BAM"
    # Add more folders as needed in the same format
)

## Sync each folder
for folder_pair in "${folders_to_sync[@]}"; do
    # Split the pair into local and remote paths
    local_path="${folder_pair%%:*}"
    remote_path="${folder_pair#*:}"
    
    echo "Syncing ${remote_user}@${remote_host}:${remote_path} to ${local_path}"
    
    # Create local directory structure
    mkdir -p "${local_path}"
    
    # Sync the folder contents from remote to local (trailing slash on source copies contents)
    rsync -av --update --progress --inplace --no-perms --no-times \
        "${remote_user}@${remote_host}:${remote_path}/" \
        "${local_path}/"
        
    echo "-----------------------------------"
done
  • Sync local folders to remote server
## Remote server details
remote_user="username"
remote_host="hpcio1" # hpc2021-io1.hku.hk 

## Define folders to sync (absolute paths)
## Format: "local_absolute_path:remote_absolute_path"
folders_to_sync=(
    "/mnt/f/Reference:/lustre1/g/path_my/Reference"
    # Add more folders as needed in the same format
)

## Sync each folder
for folder_pair in "${folders_to_sync[@]}"; do

    # Split the pair into local and remote paths
    local_path="${folder_pair%%:*}"
    remote_path="${folder_pair#*:}"
    
    echo "Syncing ${local_path} to ${remote_user}@${remote_host}:${remote_path}"
    
    # Create remote directory structure
    ssh ${remote_user}@${remote_host} "mkdir -p ${remote_path}"
    
    # Sync the folder contents (trailing slash on source copies contents)
    rsync -av --update --progress \
        "${local_path}/" \
        "${remote_user}@${remote_host}:${remote_path}/"
        
    echo "-----------------------------------"
done

Nano Text Editor

  1. Open a file with: nano filename.txt
  2. Use the arrow keys to navigate.
  3. Save the changes with ctrl + o,
  4. Confirm the filename by pressing Enter.
  5. Exit nano with ctrl + x.

Searching Text

  • To find words or phrases within a file:
  1. Initiate search with ctrl + w.
  2. Type the search term and press Enter.
  3. Exit search mode with ctrl + c.

Customizing Nano

Enhance Nano’s functionality:

nano -miA file.txt
  • -m: Enable mouse support.
  • -i: Auto-indent new lines.
  • -A: Enable syntax highlighting.

Vim Text Editor

  • Vim text editor has three main modes:
    • Normal mode: Esc, input commands
    • Insert mode: i, insert text
    • Visual mode: v, select text

Working Modes

i: Insert mode
I: Insert at beginning of line o: Insert new line below
O: Insert new line above
a: Append after cursor
A: Append at end of line
Esc: Command mode (normal)
v: Visual mode (select text)
V: Visual line mode
Ctrl + v: Visual block mode

Text Editing

Editing Shortcut
Delete char x
Delete line dd
Delete word dw
Delete to end of line d$
Delete to start of line d0
Copy line yy
Copy word yw
Paste after cursor p
Paste before cursor P
Undo u
Redo Ctrl + r
Change text c
Replace char r
Join line with next J

Search & Replace

Search & Replace Shortcut
Search text /text
Next match n
Previous match N
Search backward ?text
Search current word *

File Operations

Action Shortcut
Save :w
Quit :q
Save and quit :wq
Quit without saving :q!
Save and quit (shortcut) ZZ
Quit without saving (shortcut) ZQ

Tmux

Tmux Configuration

Consider adding these aliases to your shell configuration for quick tmux access.

# Terminal aliases for tmux
alias t="tmux"
alias ta="t a -t"
alias tls="t ls"
alias tn="t new -s"
alias tk="t kill-session -t"
alias tks="t kill-server"
Note🔧 Custom Prefix Key

Change the default prefix in .tmux.conf:

set-option -g prefix C-a
bind-key C-a send-prefix

Session Management

Action Command/Shortcut
List sessions tmux list-sessions
Attach to session tmux attach-session -t target-session
Switch between sessions Ctrl + A + s
Switch to latest session Ctrl + A + l
Detach from session Ctrl + A + d

Window Management

Action Shortcut
List all windows Ctrl + A + w
Rename current window Ctrl + A + ,
Switch to next window Ctrl + A + →
Switch to previous window Ctrl + A + ←
Create new window Ctrl + A + c
Kill current window Ctrl + A + q

Pane Management

Action Shortcut
Switch to pane above Shift + ↑
Switch to pane below Shift + ↓
Switch to pane left Shift + ←
Switch to pane right Shift + →
Kill current pane Ctrl + A + x

Copy Mode

Action Shortcut
Enter copy mode Drag mouse to select text
Paste copied text Ctrl + A + ]

Screen

Tip💡 Screen Aliases

Add these aliases to your shell configuration for easier screen management.

# Terminal aliases for screen
alias s="screen"       # start a screen session
alias ss="s -S"        # start a named screen session
alias sr="s -r"        # reattach to a screen session
alias sls="s -ls"      # list current running screen sessions

Basic Commands

Action Command
Start screen session screen
Start named session screen -S session_name
Reattach to session screen -r
List running sessions screen -ls

Window Management

Action Shortcut
Create new window Ctrl + A + C
Kill current window Ctrl + A + K
List all windows Ctrl + A + W
Go to window 0-9 Ctrl + A + 0-9
Go to next window Ctrl + A + N
Toggle between windows Ctrl + A + Ctrl + A
Rename current window Ctrl + A + A

Region Management

Action Shortcut
Split horizontally Ctrl + A + S
Split vertically Ctrl + A + \|
Switch between regions Ctrl + A + Tab
Close all regions but current Ctrl + A + Q
Close current region Ctrl + A + X

Session & Copy Mode

Action Shortcut
Detach from session Ctrl + A + D
Start copy mode Ctrl + A + [
Paste copied text Ctrl + A + ]
Show help Ctrl + A + ?
Quit screen Ctrl + A + Ctrl + \
NoteAdditional Resources

WSL

System info


## Install the neofetch package
sudo apt install neofetch -y

## Show system info
neofetch --memory_unit gib

WSL Change sudo password

In the windows terminal, run the following command to change the sudo password:


wsl -u root

## Input the new password
passwd <username>

WSL configuration

  • WSL global config: C:\Users\<UserName>\.wslconfig
  • WSL distro config: \\wsl.localhost\Ubuntu-24.04\etc\wsl.conf

Conda

Installation


# Miniforge linux
wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"

# Miniforge Mac
wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-arm64.sh"

# Install it
bash Miniforge3-$(uname)-$(uname -m).sh

# Add conda to PATH if found
if [ -f "$HOME/miniconda3/etc/profile.d/conda.sh" ]; then
    . $HOME/miniconda3/etc/profile.d/conda.sh
fi

Configuration


# Init
conda init --all

# Use mamba for faster solving
conda update -n base conda
conda install -n base conda-libmamba-solver

# Config
conda config --set solver libmamba
conda config --set always_yes true
conda config --set auto_activate_base false

# Setup channels
conda config --add channels bioconda
conda config --add channels conda-forge
#conda config --set channel_priority strict

# Install software from a specific channel
conda install -c conda-forge numpy

Environment

# Create R environment
conda create -n renv r-4.3 r-languageserver r-tidyverse r-irkernel r-httpgd

# Install bioconductor packages, all package names are lower case
conda install -n renv bioconductor-deseq2 bioconductor-edger

# Install repository packages
conda install -n renv r-qs r-fs r-tidyverse

# Remove a specific environment
conda remove --name renv --all

# Remove a software in a environment
conda remove --name renv package_name

# Export and save the conda env file with all software information
conda env export -n renv > renv.yml

# Export and save the conda env file with all software information
# without the prefix and bundle information
conda env export -n renv --no-builds > renv.yml
conda env export -n renv --no-builds --file renv.yml

# Create a new environment with a environment file
conda env create --file renv.yml

# Rename an environment
conda create --name new_env_name --clone old_env_name
conda activate new_env_name
conda remove --name old_env_name --all

Pixi

## Auto-activate pixi when entering project directory
eval "$(pixi completion --shell bash)"  # or zsh

Git

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