Unix Survival Guide

Lincoln D. Stein1

1 Department of Molecular Genetics, University of Toronto, Ontario
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Appendix 1C
DOI:  10.1002/0471250953.bia01cs51
Online Posting Date:  September, 2015
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Abstract

Most bioinformatics software has been designed to run on Linux and other Unix‐like systems. Unix is different from most desktop operating systems because it makes extensive use of a text‐only command‐line interface. It can be a challenge to become familiar with the command line, but once a person becomes used to it, there are significant rewards, such as the ability to string a commonly used series of commands together with a script. This appendix will get you started with the command line and other Unix essentials. © 2015 by John Wiley & Sons, Inc.

Keywords: Linux; Unix; shell script; command line

     
 
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Table of Contents

  • Introduction
  • Logging into a Unix System
  • Using the Command Shell
  • Managing Files and Directories
  • Working with Text Files
  • Changing the Environment
  • Installing Unix Software
  • Installing Linux
  • Conclusion
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
   Ladunga, I. 2009. Finding similar nucleotide sequences using network BLAST searches. Curr. Protoc.Bioinform. 26:3.3.1‐3.3.26.
   Stein, L.D. 2007. X Window System Survival Guide. Curr. Protoc. Bioinform. 17:A1D.1‐A.1D.11.
Key References
   Bradnam, K. and Korf, I. 2012. UNIX and Perl to the Rescue!: A Field Guide for the Life Sciences (and Other Data‐rich Pursuits). Cambridge University Press, Cambridge, U.K.
  Great introduction to the Unix command line and key tools, oriented toward the life sciences.
   Frisch, A. 2002. Essential System Administration, 3rd Edition. O'Reilly and Associates, Sebastopol, Calif.
  A more advanced guide to working on Unix systems. Although aimed at system administrators, it is highly recommended for newcomers to the Unix environment.
   Helmke M. 2014. Ubuntu Unleashed, 2014 Edition. O'Reilly and Associates, Sebastopol, Calif.
  A comprehensive introduction to the most popular Linux distribution.
   Newham, C. 2005. Learning the bash Shell: Unix Shell Programming. O'Reilly and Associates, Sebastopol, Calif.
  Learn the ins and outs of the shell itself.
   Van Vliet, J. 2011. Programming Amazon EC2. O'Reilly and Associates, Sebastopol, Calif.
  A good introduction to managing virtual machines on EC2.
Internet Resources
   http://www.bitvise.com
  Remote login packages for Windows:
   https://cyberduck.io/
  BitVise Web site. A polished terminal emulator for Windows systems using Secure Shell protocol (free for personal use).
   http://www.chiark.greenend.org.uk/~sgtatham/putty
  Cyberduck file transfer utility for Mac OS X and Windows. Supports file transfers over SSH (SFTP protocol).
   http://www.linuxmint.com
  PuTTY Web site. A simple terminal emulator for Windows systems using Secure Shell protocol (free).
   http://www.ubuntu.com
  Linux distributions:
   http://www.redhat.com
  Linux Mint, an easy‐to‐use and attractive version of Linux suitable for first‐timers (based on Ubuntu).
   http://www.centos.com
  Ubuntu, the most popular free Linux distribution, but burdened by an unfamiliar graphical user interface.
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