Upgrade to Pro — share decks privately, control downloads, hide ads and more …

Shell Scripting

2f685251aa15345f34c41c7091be99cf?s=47 Alan Orth
September 08, 2015

Shell Scripting

A session delivered to aspiring bioinformaticians as part of a workshop on bioinformatics in Nairobi, Kenya. The point of the session was to illustrate the power of shell scripting — combining simple text processing commands with logical constructs like loops — rather than trying to be a comprehensive guide.


Alan Orth

September 08, 2015


  1. Alan Orth Nairobi, Kenya September, 2015 BecA Advanced Bioinformatics Workshop

    Shell Scripting
  2. Your first shell script A shell script is a text

    file with a list of commands inside. Shell scripts are good for automating tasks you use often, or running “batch” jobs. Enter the following in a new file, call it script.sh: echo "Date and time is:" date echo "Your current directory is:" pwd
  3. Your first shell script Run the script like this: sh

    script.sh It should output something like this: "Date and time is:" Mon Aug 18 10:15:00 EAT 2052 "Your current directory is:" /home/aorth
  4. Your second shell script Create a new script, script2.sh: DATE=$(date)

    PWD=$(pwd) echo "Date and time is: $DATE" echo "Your current directory is: $PWD"
  5. Your second shell script This introduces two new concepts, variables

    and command substitution. A variable is a symbolic name for a piece of data, like text, numbers, etc. Command substitution launches a sub shell to run the named command. It’s recommended to use $(command) instead of `command`.
  6. More shell scripts A more advanced shell script utilizing a

    loop: for num in 1 2 3 do echo "We are on $num…" done What do you think it does? Can you try to run it? What is a good use case for this?
  7. Sequences Same thing, but using a “sequence”: for num in

    {1..3} do echo "We are on $num…" done This uses functionality built into the command line shell.
  8. More sequences Same result, but using a command substitution and

    the seq command. for num in $(seq 1 3) do echo "We are on $num…" done Many ways to achieve the same thing!
  9. “Globbing” (pattern expansion) Controlled by a list of files from

    the shell: DATA=/home/aorth/data/sequences for seq in $DATA/*.fastq.gz do echo "We are on $seq…" <do some science!> done
  10. I/O Redirection By default, command line programs print to stdout

    (“standard out”). I/O redirection manipulates the input/output of Linux programs, allowing you to capture it or send it somewhere else. Two main kinds of redirection: > to a file | to another program
  11. I/O Redirection Redirect the output of your script to a

    file: sh script.sh > script.out … and to another program, ie less: sh script.sh | less Voilà!
  12. Links Advanced Bash scripting guide: http://www.tldp.org/LDP/abs/html/ Excellent wiki with common

    “pitfalls”: http://mywiki.wooledge.org/BashPitfalls