Bioinformatics Laboratory at BiUH.
Core Values: Respect, Reflection, Communication, Commitment.
“GUI” stands for “Graphical User Interface”
“CLI” stands for “Command Line Interface”
Terminal: A terminal is a text-based tool that lets you control a computer or server by typing commands instead of clicking icons. It is a typical CLI.
Termius is a terminal application.
GUI: Easy, visual, slow for complex work.
CLI: Fast, powerful, hard for beginners.
Termius is the tool we use to connect to the Linux server.
Four elements for creating a new host in Termius: IP address, Port, Username, Password
Termius offers SFTP for file management (upload/download)
SSH: Secure Shell (SSH) is an encrypted network protocol used to securely access, manage, and transfer files between computers over unsecured networks
SFTP: SSH File Transfer Protocol, also known as Secure File Transfer Protocol
Position: "where you are"
Intention: "what you want to do"
File systems
Application systems
Absolute Path: The full path from the root directory to a file or folder.
Linux: /home/zhangfeng/download/test.txt
Windows: D:\download\test.txt
Relative Path: The path from your current working directory to a file or folder.
Linux: ../download/test.txt
Windows: ..\test.txt
Relative paths are shorter and faster to type than absolute paths.
They are portable (work when folders are moved/copied). They make teamwork and navigation easier, without relying on fixed root locations.
“pwd” Print working directory
“ls” List files in the current directory.
“cd” Change directories.
“cd ..” change the current working directory to its parent directory
“cd ~” change the current working directory to your home directory
“mkdir” Create directories.
“touch new_file.txt” create an empty file named new_file.txt
“less new_file.txt” view the contents of the file named new_file.txt
“cat new_file.txt” print out all contents of the file named new_file.txt
“cp original_file.txt copy_file.txt” copy the file named original_file.txt to a new file named copy_file.txt
“cp -r original_folder copy_folder” copy the contents of the folder named original_folder to a new folder named copy_folder
“mv copy_file.txt move_file.txt” move the file named copy_file.txt to a new file named move_file.txt
“mv copy_folder move_folder” move the folder named copy_folder to a new folder named move_folder
“rm tmp.txt” remove a file named tmp.txt
“rm -r tmp_folder” remove a folder named tmp_folder and all its contents recursively.
nano is a text editor that works in the linux terminal.
In nano, Ctrl + O is used to save your work
In nano, Ctrl + X is used to exit nano
“tab” type the first few letters of a file name or command, then press the Tab key. Linux will automatically complete the rest for you.
“history” You can see all the commands you have run before.
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