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)
9:00am–12:30pm Tuesday, July 17, 2018
Live coding
 Location: Portland 255
Level: Intermediate
Average rating: ***..
(3.83, 6 ratings)

Who is this presentation for?

  • Software engineers

Prerequisite knowledge

A basic understanding of bash and the command line

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”

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, which means he spends his time engineering software for bioinformatics purposes. Specifically, he develops cloud applications to enable the interactive analysis and exploration of genomics data. Robert has a PhD in bioinformatics from CSHL and a bachelor’s degree in computer engineering from McGill.

Comments on this page are now closed.

Comments

Picture of Robert Aboukhalil
Robert Aboukhalil | BIOINFORMATICS SOFTWARE ENGINEER
07/12/2018 12:10pm PDT

Yes! We’ll make the notes/slides available after the workshop.

Picture of Omer Ansari
Omer Ansari | DIRECTOR, SOFTWARE DEVELOPMENT
07/11/2018 3:39pm PDT

Robert, I can’t make it to your tutorial though i’d purchased it. any way you can share the tutorial materials?

Thanks!
Omer