Level Up Your Command Line

This session will introduce regular expressions and Linux command line tools, with an emphasis on the GNU flavored inflections of such common utilities as grep, find, sed, awk, as well as demo other well-known (and some less known) stand-bys of Bash pipelines and scripts. It will also present additional combinations of commands and tools that help perform complex tasks on the command line and otherwise streamline work. In a mixture of lecture, demos, and hands-on activities, participants will see various ways to expedite many day-to-day computing tasks, particularly tasks that involve handling structured text files (including data files and parameter files).

Learning objectives:

Participants will learn ways to improve their command-line workflow, how to read and compose regular expressions, how to use command-line tools that leverage regular expressions, and how to chain those tools together to create powerful file-processing pipelines. They will also leave with enough know-how to parse and understand the plethora of online resources that offer tips and tricks for these tools.

Knowledge prerequisites:

Basic facility with Linux and the Bash command-line. This session is not appropriate for novice or very inexperienced users.

Hardware/software prerequisites

For this session, users should also have an account on our Adroit cluster, https://researchcomputing.princeton.edu/systems/adroit (another cluster like Tiger or Della is ok), and they should confirm that they can SSH into Adroit at least 48 hours beforehand (https://researchcomputing.princeton.edu/learn/workshops-live-training/requirements-picscie-virtual-workshops).

We prefer that everyone do the session by making an SSH connection to Adroit in order to maintain a uniform environment. That said, users with a Linux or Unix command line on their own laptops are welcome to do the workshop like that. Note, however, that there can be some subtle differences in how certain commands work on, e.g., macOS vs. Linux. To minimize hiccups, Mac users are strongly encouraged to SSH into Adroit or install the GNU version of standard command line utilities using a package manager, such as homebrew (https://brew.sh/).

Session format:

Presentation, demo, and hands-on

What to expect:
Single workshop (one-off workshop –" 2 hours total)

Meet the facilitator:
Troy is an RSE working with Joshua Akey’s lab, investigating human genetic ancestry and mechanisms of evolution. Within the Lewis-Sigler Institute of Integrative Genomics, he applies rigorous software development practices to develop new analysis pipelines and improve legacy codebases. Past research areas include 3D bioprinting, single cell mass spectrometry, and mass spectrometry imaging. Troy has a B.S in Computer Science, Chemistry, Mathematics, Biochemistry and Cellular Biology and a Ph.D. in Analytical Chemistry.

To request accommodations for this event, please contact the workshop or event facilitator at least 3 working days prior to the event.

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Co-hosted with: PICSciE/Research Computing

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