Bioinfo Lab

Bioinformatics Laboratory at BiUH.

Core Values: Respect, Reflection, Communication, Commitment.

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Linux Basics

  • 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)

  • “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.