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:
- Download the Git for Windows installer here.
- 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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