Introduction to Unix

Research in biology relies increasingly on computational analyses, but state-of-the-art tools often lack a graphical user interface or web service. Use of the command line is essential for such tools, but also offers increased power and flexibility for others.

This interactive course in workshop format introduces the basics of working on the Unix command line. Participants will follow a live demonstration of command execution on their own computers and work individually on exercises covering the topics listed in the learning goals.

Learning Goals

Participants should be able to:

• Access a Unix server and use the bash interactive shell to execute commands

• Navigate and organize the file system

• Look at and search within files

• Control the input and output of commands and construct simple command chains

• Use the module system and submit jobs to a scheduling queue

Time and Place

Online at the IMB Bioinformatics Slack

Session 1: Thursday 4-5pm 09.04.20 Session 2: Tuesday 4-5pm 14.04.20 Session 3: Thursday 4-5pm 16.04.20

Required Materials

See Software Installation

Contact

Chris Field

Session 1

• The Command Line
  • Connecting to a server
  • The structure of a command
  • Useful tricks
  • Exercises
• The File System
  • Navigation
  • Exercises
  • Getting Help
  • Basic File Operations
  • Exercises

Session 2

• Working with Files
  • Looking at files
  • Exercises
  • Transferring files
  • Editing files
  • Decompressing files
  • Exercises
• Searching for and within Files
  • Wildcards
  • Searching for a file
  • Exercises
  • Searching in less
  • Regular Expressions
  • Grep
  • Exercises

Session 3

• Data Wrangling
  • Exercises
  • Combining Commands
  • Input and Output
  • Chaining programs together
  • Exercises
• The Module and Queueing Systems
  • The Module System
  • The SGE Queueing System
  • The LSF Queuing System
  • Exercises