From 082337ddad0743ba78e075d4321bc31a860dc522 Mon Sep 17 00:00:00 2001
From: Porter Libby <pelibby16@earlham.edu>
Date: Tue, 4 Feb 2025 16:19:53 -0500
Subject: [PATCH] update bash example

---
 cs-fundamentals/bash-reference-example.md | 86 +----------------------
 1 file changed, 3 insertions(+), 83 deletions(-)

diff --git a/cs-fundamentals/bash-reference-example.md b/cs-fundamentals/bash-reference-example.md
index bfd4cdf..1a332ee 100644
--- a/cs-fundamentals/bash-reference-example.md
+++ b/cs-fundamentals/bash-reference-example.md
@@ -1,95 +1,15 @@
 # Bash Reference
-Sample reference of Bash Commands<br>
-(Updated Feb 2024)
 
 ## Navigation
 - `pwd` - print work directory.
 - `ls` - list files in current directory.
   - `ls -l` - all files.
   - `ls -t` - sort files by time.
-  - `ls -a` - all files.
-  - `ls -F -l` OR `ls -Fl` - no need to have the extra space.
-  - `ls -r` - sort files by reverse order (recent at bottom).
-- `cd` - change directory.
-  - Example: `cd data-shell`.
-  - `cd ..` - go back to one directory.
-  - `cd ../../` - go to root node.
-  - `cd ~` - back to home.
-  - `cd -` - back to last one.
-  - `cd {TAB}` - complete the next.
-- `exit` = exit your shell (in the system).
 
-## File Manipulation
-- `mkdir [name]` make directory with name.
-- `cp` - copy a file.
-  - Example: `cp original.txt duplicate.txt`
-- `scp` - copy a file between two different machines over SSH.
-  - `scp [file name] [username@cluster.earlham.edu]` - copy to cluster from local computer.
-  - `scp [username@cluster.earlham.edu]:[filename]` - copy from cluster to working directory on local.
-- `mv` - move file to new location, or rename.
-  - `mv draft.txt quotes.txt` renames the file.
-  - `mv draft.txt my_folder/` moves the file to my_folder/.
-- `rmdir` - remove directory
-  - To remove a directory that is not empty: `rm -R -f [DIRECTORY]`.
-- `rm` - remove file.
 
-
-# Reading files
-- `cat` - concatenate, prints into the shell. 
-  - `cat first.dat second.dat` (concatenates first and second).
-- `wc` - word count.
-  - `wc -l` - counts lines in a file.
-- `nano filename.txt` - edit text file in the shell interface.
-- `grep` - search for text.
-  - Example: `cat myfile.txt | grep "hello"` searches myfile.txt for the string "hello".
-- `head filename.txt` - show beginning of the file.
-- `tail filename.txt` - show ending of the file.
-
-## Modules (available on cluster.earlham.edu)
-- `module avail` - lists all the pieces of software set up with module
-- `module list` - currently loaded modulefiles
-- `module load [program name]` - loads the required module
-
-## Documentation/Helpful
-- `man [command]` - get help for command
-  - use Q to quit
-- `history` - show recent commands
-- UP ARROW KEY - previous command
-
-## FOR Loops
-```
-for size in 100 200 300 400 500 600 700 800; 
-    do ./my_program $size; 
-done;
-```
-This for loop will run `my_program` eight times, each with a different "size" arguement.
-
-## Bash Scripts
- 
-```
-#! /bin/bash (It creates the ability of a file to become executable)
-{Bash commands here}
-```
- 
-chmod = change file modes or accecss control
-chmod u+x script.sh
-U = The user permission bits in the original mode of the file.
-X = The execute/search bits.
-777 = all user, all computers read and write. (absolute permissions) [chmod 777 script.sh]
-Bash ./script.sh = grant permission without chmod
- 
-The file .txt needs to be renamed to .sh
-.sh = (file extension shell)
-./script.sh (run the executable file script.sh)
-
-(To set up keys so you don’t have to enter password to switch between cluster servers) = ssh-keygen -b 2048 (Press enter without inputting anything to set everything to default)
-ssh-copy-id [username]@bronte (Enter your cluster password)
-Test → ssh whedon (to check if you need password to switch servers)
-
-rm -rf dirname = remove everything including all subdirectories and the directory itself
-Cut head -1
-mv oldname newname (renaming file)
-From shell command line: Qsub < [filename.qsub] (to run a qsub file)
+## More sections...
+- more commands...
+  - more options...
 
 
 
-- 
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