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

Description

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.

Outline

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

Arrays

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

Loops

  • The basics
  • Loop through files

Job management

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

Colors

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

Robert Aboukhalil

Invitae

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.

Leave a Comment or Question

Help us make this conference the best it can be for you. Have questions you'd like this speaker to address? Suggestions for issues that deserve extra attention? Feedback that you'd like to share with the speaker and other attendees?

Join the conversation here (requires login)

Comments

Picture of Robert Aboukhalil
Robert Aboukhalil | BIOINFORMATICS SOFTWARE ENGINEER
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