The Agave Linux Shell

Arizona State University


Dec 7, 2020

9:00 am - 3:00 pm

Instructors: Gil Speyer, Rebecca Belshe, Mollie Peters, Jason Yalim

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: Dec 7, 2020. Add to your Google Calendar.

Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email , , or for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Dec. 7th

Before Pre-workshop survey
09:00 Setup, intro, filesystem nav.
10:30 Morning break
11:00 Creating files, pipes and filters, loops
12:30 Lunch break
13:20 Scripts, queries, scheduler.
14:45 Wrap-up
15:00 END
15:00 Post-workshop Survey


To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

Access to Agave

You will need access to the supercomputer, Agave, in order to participate in the workshop. If you have not already, fill out the following web form: Agave account request.


The supercomputer must be accessed either from an on campus network or through the virtual private network (VPN) provided by Follow the directions provided by the previous webpage to connect to the VPN.

The Course Lesson

The course lesson materials are hosted here:

Supercomputer access

Either use the terminal provided by your operating system with secure shell (ssh) to connect or use the Open OnDemand webapp: