# 2022 UC Carpentries Fall Workshop (The Unix Shell)

**Workshop Details**
Dates: September 6th - 13th, 2022
Time: 9am - 12pm

**Workshop Agenda:**
https://ucsdlib.github.io/2022-09-06-carpentries-uc/

## Day 4: The Unix Shell
**Software Installation:**
**Git for Windows - Windows**
Windows: https://gitforwindows.org
* download the Git-2.33.0.2-64-bit.exe
* Git win 64 bit Direct download link https://github.com/git-for-windows/git/releases/download/v2.33.0.windows.2/Git-2.33.0.2-64-bit.exe

Mac users will use the built-in Terminal application
required for Unix Shell and Git lesson

Recommended Text editors to use:
**Nano**
* Part of Git for Windows isntaller (called GitBash)
* MacOS Terminal
**Notepad++ (optional text editor)**
* https://notepad-plus-plus.org/downloads/
* Download latest version Notepad++

**Lesson Data (download)**
* https://librarycarpentry.org/lc-shell/data/shell-lesson.zip
* Download shell-lesson.zip and move the file to your Desktop
* Unzip/extract the file. You should end up with a new folder called shell-lesson on your Desktop.

## NOTES:

**What is the shell?**
Intro slides: https://docs.google.com/presentation/d/1JvAk7a-SgYUN4y8xXtQKB2Z2iwup0hEfJZmsZ-xlJ5Q/edit?usp=sharing

**Navigating the filesystem**
Webpage for help using the shell on windows machines: http://man.he.net/

**Working with files and directories**

**Automating the tedious with loops**
More about shell scripts: https://ryanstutorials.net/bash-scripting-tutorial/

**Counting and mining with the shell**
Regular Expressions resources:
LC regex cheatsheet: https://librarycarpentry.org/lc-data-intro/reference.html
regex101:https://regex101.com/
regexper: https://regexper.com/
Regex Testing: https://www.regextester.com/

## Workshop Day 4
### First name and Last Name/Organization/Dept./Email
| Name (first & last) | Organization | Dept. | Email |
| ------------------------- | ------------ | ----- | --------------- |
| (example) Jane Doe | UCSD | IT | [e-mail] |
|Tom Le|UCM||[e-mail]|
|John Thompson |UC Merced |Cell & Molecular Biology |[e-mail] |
|Sam Erickson |UC Merced |Physics |[e-mail] |Dilawer Ali | UCM |Mehcanichanical Engineering |[e-mail]
|Sarina Qin |UC Merced |Nat Sci |[e-mail] |
|Douglas Zhang |UCSD |Chemistry and Biochemistry |[e-mail] |
|Kenan Chan |UCSD |SIO |[e-mail] |
| Bruce Hamilton |UCSD |CMM|[e-mail] |
|Jonathan Le |UCR |Mathematics |[e-mail] |
|Amber Heidbrink |UCSD |Cell and Developmental Biology |[e-mail] |
|Dayana Elizalde |UCR | |[e-mail] |
| Shang Su|U Toledo | Cell and Cancer Biology| [e-mail]|
|Christopher Gray |UCR |Computer Sciencee |[e-mail] |
|Oishee Misra |UCSD |Economics |[e-mail] |
|Ha Vu |UCSD |Economics |[e-mail] |
|Michelle Wu |UCLA |Neuroscience |[e-mail] |
|Jay Chi | UCSB |ETS |[e-mail] |
|Osika Tripathi |UCSD |PUblic Health |[e-mail] |
|Kazuma Nagatsuka |UCSD |Robotics(Mechanical Engineering) |[e-mail] |
| Melodi Frey| UCSD|CMM |[e-mail] |
|Matthew Falcone |UCB |Civil and Environmental Engineering | [e-mail]|
|Ivan Felix Rios | UCSD|Mathemathics & Economics | [e-mail]|
|Brett Taylor |UCSD |Biomedical Sciences |[e-mail] |
| Agnieszka Pluta| UCLA| Psychology| [e-mail]|
|Jun Tan|UCSD |Economics |[e-mail]
| Roberto Silva | UCSD | Scripps | [e-mail] |
|Vishakha Malhotra|UCSF|Biostatistics and Epidemiology|[e-mail]
|Lillie Pennington|UC Merced|Life and Environmental Sciences|[e-mail]
|Alexander Frey|UCSD|Rady School of Management| [e-mail]
|Cherie Thompson|UCSD Library
|Dexin Zhou|UCSD|Mathematics|[e-mail]|
|Nicole Rosenberg|UCSD|Scripps|[e-mail]|
|Mugen Blue|UCM|EECS|[e-mail]|
|Haley Potts|UCSD|Math & Economics|[e-mail]
|Aleks Leszczynska|UCSD|Pediatrics|[e-mail]
|Junxiao Gao|UCSF|Biostatistics and Epidemiology|[e-mail]
|Steven Krehel|UCSD|Economics|[e-mail]
|Zhaoning (Johnny) Wang|UCSD|CMM|[e-mail]|
|Daryl Han|UC Irvine|Student Center and Event Services|[e-mail]|
|Josiah Piceno |UCM |MBSE |[e-mail] |
|Apisit Kaewsanit |UCSF|Epidemiology and Biostatistics|[e-mail]|
|Jacob Ross|UCSD|anesthesiology|[e-mail]|
|Jay Colond|UCM|sociology|[e-mail]|
|Anshika Kandhway|UCM|Environmetal System|[e-mail]|
|Dilawer Ali|UCM|Mechanical Engineering|dali4@|
|Bineh Ndefru|UCLA|Materials Science|[e-mail]|
|Mario Cuaya|UCR|Computer Science|[e-mail]|
|Andrew Chan|UCSD|IGPP|[e-mail]|
|Andrew Gorin|UC Berkeley|Earth and Planetery Science|[e-mail]|
|Donald Zarate| UCR | Political Science and Psychology | [e-mail] |
|Jessica Wu-Woods|UCR|Microbiology|[e-mail]|
|||||
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## Day 4 Exercises
1. **Copying a file**
Instead of moving a file, you might want to copy a file (make a duplicate), for instance to make a backup before modifying a file. Just like the mv command, the cp command takes two arguments: the old name and the new name. How would you make a copy of the file gulliver.txt called gulliver-backup.txt? Try it!

2. **Renaming a directory**
Renaming a directory works in the same way as renaming a file. Try using the mv command to rename the firstdir directory to backup.

3. **Moving a file into a directory**
If the last argument you give to the mv command is a directory, not a file, the file given in the first argument will be moved to that directory. Try using the mv command to move the file gulliver-backup.txt into the backup folder.

4. **For loop exercise**
Complete the blanks in the for loop below to print the name, first line, and last line of each text file in the current directory.

___ file in *.txt
___
    echo "_file"
    head -n 1 _____
    ____ __ _ _____
___

5. **Count, sort and print (faded example)**
To count the total lines in every tsv file, sort the results and then print the first line of the file we use the following:

wc -l *.tsv | sort -n | head -n 1

Now let’s change the scenario. We want to know the 10 files that contain the most words. Fill in the blanks below to count the words for each file, put them into order, and then make an output of the 10 files with the most words (Hint: The sort command sorts in ascending order by default).

__ -w *.tsv | sort __ | ______
6. **Counting number of files**
Let’s make a different pipeline. You want to find out how many files and directories there are in the current directory. Try to see if you can pipe the output from ls into wc to find the answer.

7. **Counting the number of words**
Check the manual for the wc command (either using man wc or wc --help) to see if you can find out what flag to use to print out the number of words (but not the number of lines and bytes). Try it with the .tsv files.
If you have time, you can also try to sort the results by piping it to sort. And/or explore the other flags of wc.

8. **Case sensitive search in select files**
Search for all case sensitive instances of a word you choose in the ‘America’ and ‘Africa’ .tsv files in this directory. Print your results to the shell.

9. **Count words (case sensitive)**
Count all case sensitive instances of a word you choose in the ‘America’ and ‘Africa’ .tsv files in this directory. Print your results to the shell.

10. **Case insensitive search in select files (whole word)**
Search for all case insensitive instances of that whole word in the ‘America’ and ‘Africa’ .tsv files in this directory. Print your results to a file results/hero-i.tsv.

## Day 4 Reflection
Please enter how you will use the Unix Shell in your work or research here:
1. As a sysadmin, I use the shell everyday with SSH. Move and migrate data all the time with tools like rsync. Getting to the point where I prefer to manage files/folders with shell rather than macOS GUI. Many of the commands from the workshop were familiar, but defintely found some very helpful additional commands to help manage my systems more efficiently (i.e. CTRL-r). Thanks!

## Day 4 Survey
Link to survey for today: https://forms.gle/5qgx8X6H3GRMacwD6

## Day 4 Questions
Please enter any questions not answered during live session here:
1.

### End Day 4