Workshop Description (Intermediate Course)

This workshop (UNIX Command Line II) continues Workshop W1: UNIX Command Line I and uses the Hoffman2 campus computing cluster.  The focus is on features that make dealing with large files or large numbers of files or repetitive tasks easier.  These include shell variables, substitutions, redirections, pipes, loops, conditionals, subshells, shell functions, and shell scripts.  There will be illustrations of how to run modest numbers of multiple commands at the same time — both within a single node/one computer, and (using the Hoffman2 queue system) across multiple nodes of the cluster.

Workshop Materials

Review UNIX I; shell features

More shell features

Hoffman2 queue system

Technical Requirements

  • Hoffman2 Cluster Access is required.


Dr. Shawn Cokus is an Associate Researcher in the Department of Molecular, Cell, and Developmental Biology. Dr. Cokus has been doing bioinformatics at UCLA since 2002, and his interests include methods for BS-Seq, RNA-Seq, Hi-C, and protein-protein interaction prediction. His recent work focuses on de novo genome assembly and annotation. Dr. Cokus earned a Ph.D. in Mathematics from the University of Washington. Email:



Workshop Details

Prerequisites: Intro to UNIX Command Line (W1)
Length: 3 days, 3 hrs per day
Level: Advanced
Location: Boyer 529
Seats Available: 28

Spring 2024 Dates

April 16, 17, and 18
1:30 PM – 4:30 PM