Put open source to work
July 16–17, 2018: Training & Tutorials
July 18–19, 2018: Conference
Portland, OR

You don't know bash.

Robert Aboukhalil (Invitae)
9:00am12:30pm Tuesday, July 17, 2018
Live coding
Location: Portland 255
Level: Intermediate

Who is this presentation for?

  • Software engineers

Prerequisite knowledge

  • A basic understanding of bash and the command line

Materials or downloads needed in advance

  • A Linux laptop

What you'll learn

  • Learn how to build standalone and library bash tools, use functions and arrays, and manage processes using command-line tools


On most days, bash is a great tool for quick-and-dirty file manipulation and system management. Join Robert Aboukhalil to learn how the command line allows you to do a whole lot more, including arrays, functions, parsing JSON, and process substitution.


Building standalone scripts

  • The basics
  • How to parse user input
  • Functions
  • How to “import” your bash scripts

String manipulation

  • The basics
  • Regular expressions in pure bash
  • How to parse JSON
  • Math calculations in bash


  • The basics
  • Reading a file into an array
  • Array ranges


  • The basics
  • Loop through files

Job management

  • Process management
  • Screens
  • Process substitution
  • Parallelize jobs using xargs


  • How to output colors on the command line
Photo of Robert Aboukhalil

Robert Aboukhalil


Robert Aboukhalil is a bioinformatics software engineer at Invitae, where he develops cloud applications for the analysis and interactive visualization of genomics data. Robert holds a PhD in bioinformatics from Cold Spring Harbor Laboratory and a BEng in computer engineering from McGill.

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Picture of Robert Aboukhalil
06/01/2018 12:47pm PDT

For a sneak peak of what you’ll learn at this workshop, make sure to check out my article about “The wondrous world of Bash arrays”: https://opensource.com/article/18/5/you-dont-know-bash-intro-bash-arrays