Video Recordings

Videos for BCH519 Unit 2 can be found at:

https://buffalo.edu/~aebruno2/teaching/bch519

Outline for this lecture

• What is Linux?
• CCR OnDemand
• Command Line Boot Camp
• Edit files

An operating system is a collection of software that manages computer resources

Operating Systems

• Linux
• Windows
• macOS, iOS, watchOS
• Android, Chromium OS
• Orbis OS

A very brief history of UNIX…

UNIX

• Originally developed in 1969 at AT&T Bell Labs
• First ran on the PDP-11/20 16-bit minicomputer
• Widely adopted in academia

UNIX Features

• Multi-user, multi-tasking, time-sharing
• Large number of users to interact concurrently with a single computer
• Consists of many utility programs or commands
• Master control program called the kernel
• Use plain text for storing data
• Hierarchical file system

UNIX Philosophy

• Write programs that do one thing and do it well
• Write programs to work together
• Write programs to handle text streams, because that is a universal interface

UNIX has many descendents..

Linux

Linux

• A “UNIX-Like” operating system
• GNU Project started in 1983 by Richard Stallman, to create “complete UNIX-compatable software system” composed entirely of free software
• Linux kernel first developed by Linus Torvolds in 1991
• Together they make the GNU/Linux operating system
• Free and open source

Many flavors of Linux

Linux on the Desktop

Linux in the Data Center

Linux is Everywhere

Why Linux for this Course?

• Many research centers run Linux
• Popular in Bioinformatics
• Includes many programming languages and environments
• CCR operates a data center with hundreds of Linux computers
• To run jobs at CCR, you need to be familiar with Linux

Getting started with Linux

• Install Linux on your Desktop/Laptop (Local)
• Run Linux off Live USB
• Connect to remote Linux server (Remote)

Linux - Remote Login

• Connect to remote Linux server
• We use SSH: Secure SHell
• Allows us to connect to remote Linux server using encrypted network channel
  • MobaXTerm (Windows)
  • OpenSSH (Linux/Mac OS X)
  • CCR OnDemand (Web based)

CCR OnDemand

• Easy to use web-based portal for HPC resources
• Shell access to CCR Linux servers using web browser
• Uses SSH under the hood
• https://ondemand.ccr.buffalo.edu

CCR OnDemand Shell Access

CCR OnDemand Shell Access

Operating systems have user interfaces

• GUI - Graphical User Interface
• CLI - Command Line Interface

CLI - Command Line Interface

• Control the computer with commands
• “Shell” - a program that accepts commands and performs operating system functions
• We’ll be using a shell called BASH

Anatomy of the shell

• There’s a prompt: [aebruno2@vortex1:~]$
• You type in commands
• Shell executes the commands
• Prints output to the screen
• Repeat

How to read the SHELL

Anatomy of a command

• Basic form: command options arguments
• command = name of the command
• options = modify the behavior of the command
• arguments = expression or filename
• Commands can be simple: echo, date
• More complex: find . -type f -name \*.py

Command Line Boot Camp

Simple Commands

Print todays date

$ date
Mon Jan 28 13:24:03 EST 2019

Echo a string

$ echo "Hello World"
Hello World

Simple Commands

What’s my username?

$ whoami
aebruno2

What computer am I logged into?

$ hostname --fqdn
srv-p22-13.cbls.ccr.buffalo.edu

Getting Help

• man page (short for manual page)
• Usage: man [command name]

$ man echo
$ man grep

Download and print!

GNU Coreutils Cheat Sheet

http://www.catonmat.net/download/gnu-coreutils-cheat-sheet.pdf

Files, Directories, and Paths

• Basic unit is a File
• Files are organized in directories (folders)
• Navigate filesystem using paths

Hierarchical Filesystem

/home/aebruno2/bch519/hello.py

Moving around

• Print the current working directory: pwd
• List all files: ls
• Change working directory: cd
• Move up a directory (go back): cd ..

$ pwd
/user/aebruno2
$ ls
projects bch519 docs hello-world.txt
$ cd bch519
$ pwd
/user/aebruno2/bch519
$ ls
hello.py test.py README.txt
$ cd ..
$ pwd
/user/aebruno2

File Basics

• Create a file: touch
• Copy files: cp
• Rename files: mv
• Remove files: rm
• View files: cat,less,more

$ touch hello-world.txt
$ ls
hello-world.txt
$ cp hello-world.txt goodbye-world.txt
$ ls
hello-world.txt goodbye-world.txt
$ mv goodbye-world.txt new-file.txt
$ rm goodbye-world.txt
$ cat hello-world.txt
Hello World!

Text Manipulation

• Search for patterns in file: grep
• Print first/last n lines: head, tail
• Count lines, words, characters: wc
• Print selected parts of file: cut
• Sort file: sort

$ grep "pattern" my_file
$ head -n 20 my_file
$ tail -n 20 my_file
$ wc -l my_file
$ cut -f 1,3 my_file
$ sort my_file

Input/Output redirection

• > takes output from command and writes it to file
• >> takes output from command and appends it to file
• < takes input from file and sends it to command

$ echo "Hello World" > hello.txt
$ cat hello.txt
Hello World
$ echo "Goodbye" >> hello.txt
$ cat < hello.txt
Hello World
Goodbye
$ grep "Hello" hello.txt > results.txt
$ cut -f 1,3 output.txt > columns-1-3.txt

Pipes

• Allows you to “chain” commands together
• | = pipe
• | take output from command on left and send as intput to command on right

$ cat my_file.txt | wc -l
$ cat my_file.txt | grep -i "hello"
$ echo "Hello World" | wc -c > num-chars.txt
$ echo "1234" | rev
4321

Editing Files

• Editor: A program for editing text files
• Most important tool for programmers
• We will use an editor to author Python programs

Editors

GNU nano

• Simple text editor
• Controlled using the control key (Ctrl)
• Documentation:

http://www.nano-editor.org/docs.php

GNU nano basics

• Start: nano <filename>
• ^ = Ctrl key
• Save file: ^O
• Quit: ^X
• Search: ^W
• Help: ^G

GNU nano

Homework #1

Due: 2021-02-16 09:00:00