Essential UNIX Skills for Biologists

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Essential UNIX Skills for Biologists

• Yannick Pouliot, PhD
• Bioresearch Informationist
• Lane Medical Library Knowledge Management
  Center
• 8/14/2008

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The Bioresearch Informationist At Your Service

• Yannick Pouliot, PhD, Lane Medical Library
  Knowledge Management Center
• Bioresearch Informationist computational
  biologist in residence
• Lane Library service
• Closely coordinated with CMGM
• Role Support laboratory researchers regarding
  biocomputational resources and their use
• especially postdocs
• Contact lanebioresearch_at_stanford.edu

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Goals

• Deliver basic understanding of core UNIX commands
• Tips on running UNIX on Mac and Windows

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But First LaneConnex -- Your Key to Finding
Resources Quickly
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Why UNIX?

• UNIX is good for
• performing operations with very few key strokes
• operating on large number of objects for e.g.,
• searching file contents very specifically
• renaming files
• moving/copying files
• UNIX is fast
• LINUX( UNIX) is free and runs on everything

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UNIX Trip-Ups

• UNIX is capitalization-sensitive
• ls ? Ls
• What you type is what you get
• no mistyping!
• mind those commands
• e.g., rm fr delete everything below the
  current directory! ? DONT DO THIS AT HOME!

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So How Does One Access UNIX?

• Mac UNIX underlies Macs graphical interface
• access Applications ? Utilities ? Terminal
• Windows Must install code (more later)

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Exploring UNIX
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Key Concepts

• UNIX is command-line based (no cute icons).
• There are flavors of UNIX
• Linux UNIX
• Shell command line interface
• different shells exist, all with identical basic
  functionality
• Anything you can imagine, UNIX can do
• but you may have to think about it
• In UNIX, anything can be done in at least three
  different ways
• UNIX has
• commands (built-in) ? most of todays workshop
• utilities
• super-commands, e.g., grep, for parsing text
• not built-in but usually there

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Concept Redirection

• Redirection operator
• gt or lt add to file (overwrite)
• gtgt or ltlt add to file (dont overwrite)
• Applies to both input and output
• file.txt gt prog.exe
• prog.exe gt file.txt
• File.txt gt prog.exe gt file1.txt
• prog.exe gtgt file.txt

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Concept Metacharacters

• 0 or more characters of any kind
• . exactly one character of any kind
• Metacharacters can be used with nearly any other
  command, e.g.,
• ls file?.txt
• ls file.txt
• ls .
• more .txt
• grep omics .txt
• NB There are lots of other kinds of
  metacharacters

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Concept Stringing Commands Together Using Pipes

• I pipe, e.g.
• ls -1 more

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Overview of Selected UNIX Commands
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• ls options names
• List contents of directories, including
  directories themselves
• Basically, lists files
• When names are provides, lists files contained in
  a directory name or that match a file name.
• names can include filename metacharacters.
• The options display information in different
  formats. The most useful options include -F, -R,
  -l, and -s.
• Examples
• 1. list all details of all files in current
  directory
• ls l
• 2. list just the filenames
• ls -1
• 3. create a file that contains a list of the
  filenames
• ls -1 gt mylist.txt

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cat/more/head/tail

• ? commands to look at content of files
• cat returns everything
• more same but one page at a time
• head returns top x lines
• tail returns bottom x lines
• all can operate on multiple files
• Examples
• 1. show contents of all txt files
• cat .txt
• 2. show first 100 lines of file
• head 100 file.txt
• 3. show first 1000 lines of file and paginate
• head 1000 file.txt more

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grep Searching File Contents Using Regular
Expressions

• grep options pattern files
• Searches files for presence of a string
• grep protein .pdf
• about a million options
• Also searches using regular expressions
• Definition a mathematical expression that
  expresses the characteristics of one or more
  strings, e.g.
• te?xt
• omics

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• find pathnames conditions
• Very powerful can specify anything, including
  exclusions and negations
• Descends the directory tree beginning at each
  pathname and locates files that meet the
  specified conditions. The default pathname is the
  current directory.
• Most useful conditions are -name and -type (for
  general use)
• Examples
• 1. List all files named chapter1 in the /work
  directory
• find /work -name chapter1
• 2. Look for filenames in current directory that
  don't begin with a capital letter
• find . ! -name 'A-Z'

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UNIX on Windows

• Easy UnxUtls
• UNIX light
• Excellent for most tasks
• Not a complete emulation of UNIX
• Hard Cygwin
• difficult to make it behave perfectly
• can run in parallel with Windows
• Easier dual boot
• ability to boot either Windows or Linux
• requires reboot

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Resources

• UNIX commands http//en.wikibooks.org/wiki/Guide_
  to_Unix/Commands
• Another list of UNIX utilities
  http//en.wikipedia.org/wiki/List_of_Unix_utilitie
  s

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Everything You Need to Know About UNIX in Short
Form eBooks from Lane

• The ultimate quick reference for LINUX
• More than you typically need, but you can zoom
  into what you need

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