Advanced Beginner Shell

Who: Titus Brown and Lisa Cohen, instructors; Shannon Joslin, TA.

When: January 30, 2017

Times: 9:15am-12:15pm PST

Where: 1043 Valley Hall, UC Davis Campus

Contact: Please contact Titus Brown

Description

This half-day workshop will continue from the end of the Beginning Shell lesson (see materials here: https://github.com/ngs-docs/2015-shell-genomics/blob/gh-pages/README.rst).

The new materials are here (also linked above)

We will cover loops, if statements, scripting, and I/O redirection (>, <, etc.). We will also talk a bit about how to put together shell scripts for job submission on queuing systems (‘qsub’ etc.).

Installation instructions

The Bash Shell

Windows:

  1. Download the Git for Windows installer here.
  2. Follow install instructions.
    • Click “next”
    • Click “next”
    • Click “next”
    • Click “next”
    • Click “next”
    • Select “Use Git from the Windows Command Prompt” and click on “next”. If you forget to do this, re-run the installer and select the correct option.
    • Click “next”, keep “Checkout Windows-style, commit Unix-style line endings” selected.
    • Select “Use Windows’ default console window” and click on “next”
    • Click on “next”
    • Click on “finish”

Mac OS X:

The default shell in Mac OS X is bash, so you can access the Terminal from /Applications/Utilities (go to your Applications folder, then go to the Utilities window. You should see “Terminal” there)


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