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Day2: Intro to Linux

Day2: Intro to Linux

Welcome to Day 2 of the Short-Read Sequencing Analysis Workshop. The videos for Day 2 will serve as an introduction to the Linux/Unix environment. After watching the 5 videos you should have some understanding of how we use our local machine to connect and communicate with a remote server or compute cluster, be able to perform basic Linux commands, understand the hierarchical file system of the server, and have an introduction to the text editor VIM.

Videos for Day 2

Video 1: Introduction to Linux (9:11)  This video will give a brief background on the Linux operating system, and how to access a remote server on both a PC and Mac.

Video 2: Working on a Linux System (12:37)  This video aims to give a basic understanding of the hierarchical file system on the server, understanding the concept of at PATH, and introduce some basic Linux commands such as pwd, cd, and ls.

Video 3: Linux Commands for File Manipulation (10:03)  This video introduces basic Linux commands to create, copy, move, and delete files and directories, as well as ways to view files.

Video 4: Important Linux Skills (16:37)  This video shows how to view and use command manuals, find and use command options, and learn command input/output including stdout, stderr, capturing output, and piping.

Video 5: VIM Text Editor (11:53)  The last video in this series introduces the VIM text editor that will be used throughout most of the other videos as well as in-class. Other editors may be used but we will try to limit our examples to VIM.

Supplementary Video: Command Line History and Permissions (5:31)  This supplementary videos shows you how to access the command line history, and explains how permissions work for directories and files on the server


Files for Day 2

Day2 Cheat sheet, contains common Linux commands, I/O information, and some common VIM commands. We recommend bringing this sheet in to class each day.

Day 2 Homework Revised - this is the homework we revised due to the in-class complications with rsync

Day 2 Homework 

Day 2 Homework Answers - These are the answers to the original homework, the revised homework didn't include the first question.

Day 2 In-class Slides

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