The Unix Shell

The Jackson Laboratory

Dec 9 & 16, 2019

1:00 pm - 4:00 pm

Instructors: Sue McClatchy

Helpers:

General Information

The Unix shell has been around longer than most of its users have been alive. It has survived so long because it’s a power tool that allows people to do complex things with just a few keystrokes. More importantly, it helps them combine existing programs in new ways and automate repetitive tasks so they aren’t typing the same things over and over again. Use of the shell is fundamental to using a wide range of other powerful tools and computing resources (including “high-performance computing” supercomputers). These lessons will start you on a path towards using these resources effectively.

Prerequisites This lesson guides you through the basics of file systems and the shell. If you have stored files on a computer at all and recognize the word “file” and either “directory” or “folder” (two common words for the same thing), you’re ready for this lesson.

If you’re already comfortable manipulating files and directories, searching for files with grep and find, and writing simple loops and scripts, you probably want to explore the next lesson: shell-extras on December 16.

The workshop will be held for two consecutive Monday afternoons from 1pm to 4pm on Dec 9 & 16 at the Jackson Laboratory campuses in Bar Harbor, Maine and Farmington, Connecticut. Participants must attend in person. Remote attendance from desks, home, or away will not be supported.

Bar Harbor: breezeway bioinformatics training room 1540, building 1, unit 5

Farmington: conference room 3320

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".

Where: Bioinformatics Training Room, 600 Main Street, Bar Harbor, Maine | Room 3320, Farmington CT. Get directions with OpenStreetMap or Google Maps.

When: Dec 9 & 16, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). They should have a few specific software packages installed (listed below).

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.

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.


Surveys

Please be sure to complete this survey after the workshop.

Post-workshop Survey


Schedule

Monday, December 9

13:00

Automating Tasks with the Unix Shell

14:30

Afternoon break

15:00

Automating Tasks with the Unix Shell (Continued)

15:55

Wrap-up

16:00

END


Monday, December 16

13:00

Shell features

14:30

Afternoon break

15:00


Shell features (Continued)

15:45

Wrap-up

15:50

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


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.

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.

The Bash Shell

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

The Bash Shell

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

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. From the dropdown menu select "Use the nano editor by default" and click on "Next".
    3. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
    4. Ensure that "Use the native Windows Secure Channel library" is selected and click on "Next".
    5. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    6. Ensure that "Use Windows' default console window" is selected and click on "Next".
    7. Ensure that "Enable file system caching" and "Enable Git Credential Manager" are selected and click on "Next".
    8. Click on "Install".
    9. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

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.

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, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

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.

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 BBEdit or Sublime Text.

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.

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). You may want to keep Terminal in your dock for this workshop. 

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. 

JAX provides access to high performance computing (HPC) through the Helix cluster, which currently serves Farmington and Bar Harbor.

Cluster Access

Ask the JAX IT Service Desk to give you an account for Helix.