The Jackson Laboratory for Genomic Medicine

Dec 7, 2018

9:00 am - 4:00 pm

Instructors: Shane Sanders, Dave McKenzie, Jason Macklin

Helpers: Bill Flynn, Neil Kindlon, Sandeep Namburi

General Information

This workshop is only open to Jackson Laboratory employees.

Where: Holt Conference Room 1405, 10 Discovery Dr, Farmington CT. Get directions with OpenStreetMap or Google Maps.

When: Dec 7, 2018. Add to your Google Calendar.

Requirements: Participants must bring a laptop 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). They are also required to abide by Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email susan.mcclatchy@jax.org for more information.


Schedule

Day 1

Before Pre-workshop survey
09:00 Welcome and introductions
09:15 Introducing the Shell
09:20 Navigating Files and Directories
10:00 Working With Files and Directories
10:30 Coffee
10:45 Working With Files and Directories (continued)
11:05 Pipes and Filters
12:00 Lunch break
13:00 JAX Cluster Resources
14:30 Coffee
14:45 JAX Cluster Resources (continued)
15:45 Post-workshop survey
16:00 END

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


Syllabus

The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...

Setup

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

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

  1. Ask the JAX IT Service Desk to download and install PuTTY.

macOS

The default shell in all versions of macOS is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

Linux

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, try typing the escape key, followed by :q! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

Windows

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

macOS

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are Text Wrangler or Sublime Text.

Linux

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

High Performance Computing Cluster

JAX provides access to high performance computing (HPC) through two computing clusters: 1) Cadillac, which serves Bar Harbor; and 2) Helix, which serves Farmington.

Cluster Access

Ask the JAX IT Service Desk to give you an account for Cadillac (Bar Harbor) or Helix (Farmington).