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‎README.md

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- [Introducing the shell](#introducing-the-shell)
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- [Reasons to use the shell](#reasons-to-use-the-shell)
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- [\"Unix\"](#unix)
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- [\"Shell\"](#shell)
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- [The past is always with us](#the-past-is-always-with-us)
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- [So what is a \"shell\"?](#so-what-is-a-shell)
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- [Navigating files and
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directories](#navigating-files-and-directories)
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- [File system layout](#file-system-layout)
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- [Simplify your loop with globs](#simplify-your-loop-with-globs)
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- [Generalize your loop with unlimited
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arguments](#generalize-your-loop-with-unlimited-arguments)
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- [Make your script executable](#make-your-script-executable)
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- [Finding things](#finding-things)
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- [Find](#find)
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- [Grep](#grep)
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- [Shell extras](#shell-extras)
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- [SSH](#ssh)
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- [Permissions](#permissions)
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- [Job control](#job-control)
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- [Aliases and bash
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customization](#aliases-and-bash-customization)
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- [More on shell variables](#more-on-shell-variables)
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- [Mini-languages (grep, sed, AWK)](#mini-languages-grep-sed-awk)
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- [Shell expansion](#shell-expansion)
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- [Conditional tests](#conditional-tests)
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- [Credits](#credits)
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- [References](#references)
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- [Data Sources](#data-sources)
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# Introducing the shell
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Powerpoint slides: \"Automate all the things!\"
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## Reasons to use the shell
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1. Automate basic tasks
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2. Underlies many other open source languages and applications; knowing
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the shell will make you better at using them
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3. System administration, HPC, and remote computing
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4. Many special-purpose tools become available to you
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2. Underlies many other open source languages and applications and can
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be used to glue them together
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3. Essential for system administration, remote computing, and
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high-performance computing
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4. Many concise special-purpose tools that can make your life easier
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5. Complements more fully-featured application programming languages
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## The past is always with us
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## \"Unix\"
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The design and terminology of modern computers is based on metaphors
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from a previous age.
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Powerpoint slides: Unix family tree
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1. Files and folders
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2. Teletype input and output
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3. Modern touch devices don\'t expose the file system, so you may be
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less comfortable with navigating directory trees than people whose
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primary computing devices were desktop computers
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1. Unix-like operation systems share a common architecture and layout
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2. Roughly compatible, with similar (or identical) shells and tools
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3. The environment in which most open-source software was written
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## So what is a \"shell\"?
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## \"Shell\"
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- Broadly speaking, there is a tension between making computer systems
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fast and making them easy to use.
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It provides a simple interface for making the operating system do
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work, without having to know exactly how it accomplishes that work.
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## The past is always with us
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The design and terminology of modern computers is based on metaphors
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from a previous age.
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1. Files and folders
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2. Teletype input and output
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3. Modern touch devices don\'t expose the file system, so you may be
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less comfortable with navigating directory trees than people whose
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primary computing devices were desktop computers
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# Navigating files and directories
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## File system layout
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bash aggregate.sh ../proteins/*.pdb
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```
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## Make your script executable
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``` bash
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# List file in long format to show current permissions
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ls -l aggregate.sh
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# Change file mode (i.e. permissions)
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# User can read/write/execute, Group and Other can read
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chmod u=rwx,go=r aggregate.sh
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# Show changed permissions
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ls -l aggregate.sh
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# Invoke script
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./aggregate.sh ../proteins/*.pdb
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```
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# Finding things
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## Find
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## Grep
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# Shell extras
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## SSH
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## Permissions
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## Job control
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TBD
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## Aliases and bash customization
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## More on shell variables
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## Mini-languages (grep, sed, AWK)
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## Shell expansion
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# Shell extras
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## Conditional tests
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Consult the Wooledge Bash Guide (see references below) for more on these
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topics:
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1. SSH
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2. Permissions
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3. Job control
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4. Aliases and bash customization
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5. Shell variables
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6. Mini-languages (grep, sed, AWK)
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7. Shell expansion
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8. Conditional tests
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# Credits
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‎README.org

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#+TITLE: Unix Shell
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#+AUTHOR: Derek Devnich
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#+BEGIN_SRC bash
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#+END_SRC
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#+BEGIN_EXAMPLE
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#+END_EXAMPLE
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* Introducing the shell
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Powerpoint slides: "Automate all the things!"
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** Reasons to use the shell
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1. Automate basic tasks
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2. Underlies many other open source languages and applications; knowing the shell will make you better at using them
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3. System administration, HPC, and remote computing
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4. Many special-purpose tools become available to you
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2. Underlies many other open source languages and applications and can be used to glue them together
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3. Essential for system administration, remote computing, and high-performance computing
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4. Many concise special-purpose tools that can make your life easier
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5. Complements more fully-featured application programming languages
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** "Unix"
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Powerpoint slides: Unix family tree
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1. Unix-like operation systems share a common architecture and layout
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2. Roughly compatible, with similar (or identical) shells and tools
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3. The environment in which most open-source software was written
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** "Shell"
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- Broadly speaking, there is a tension between making computer systems fast and making them easy to use.
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- A common solution is to create a 2-layer architecture: A fast, somewhat opaque core surrounded by a more friendly scriptable interface (also referred to as "hooks" or an "API"). Examples of this include video games, Emacs and other highly customizable code editors, and high-level special-purpose languages like Stata and Mathematica.
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- Unix shell is the scriptable *shell* around the operating system. It provides a simple interface for making the operating system do work, without having to know exactly how it accomplishes that work.
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** The past is always with us
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The design and terminology of modern computers is based on metaphors from a previous age.
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1. Files and folders
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2. Teletype input and output
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3. Modern touch devices don't expose the file system, so you may be less comfortable with navigating directory trees than people whose primary computing devices were desktop computers
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** So what is a "shell"?
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- Broadly speaking, there is a tension between making computer systems fast and making them easy to use.
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- A common solution is to create a 2-layer architecture: A fast, somewhat opaque core surrounded by a more friendly scriptable interface (also referred to as "hooks" or an "API"). Examples of this include video games, Emacs and other highly customizable code editors, and high-level special-purpose languages like Stata and Mathematica.
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- Unix shell is the scriptable *shell* around the operating system. It provides a simple interface for making the operating system do work, without having to know exactly how it accomplishes that work.
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* Navigating files and directories
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** File system layout
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Powerpoint slides: "Navigating files and directories"
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bash aggregate.sh ../proteins/*.pdb
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#+END_SRC
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** Make your script executable
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#+BEGIN_SRC bash
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# List file in long format to show current permissions
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ls -l aggregate.sh
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# Change file mode (i.e. permissions)
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# User can read/write/execute, Group and Other can read
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chmod u=rwx,go=r aggregate.sh
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# Show changed permissions
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ls -l aggregate.sh
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# Invoke script
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./aggregate.sh ../proteins/*.pdb
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#+END_SRC
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* Finding things
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** Find
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*** Find everything
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#+END_SRC
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** Grep
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TBD
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* Shell extras
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** SSH
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** Permissions
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** Job control
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** Aliases and bash customization
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** More on shell variables
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** Mini-languages (grep, sed, AWK)
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** Shell expansion
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** Conditional tests
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Consult the Wooledge Bash Guide (see references below) for more on these topics:
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1. SSH
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2. Permissions
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3. Job control
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4. Aliases and bash customization
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5. Shell variables
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6. Mini-languages (grep, sed, AWK)
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7. Shell expansion
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8. Conditional tests
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* Credits
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1. The Unix Shell: https://swcarpentry.github.io/shell-novice/

‎_config.yml

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title: Unix Shell
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description: Class notes and code examples
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remote_theme: jekyll/minima

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