From aad7109b5ee62f58c4cdc806e25019da733d4d72 Mon Sep 17 00:00:00 2001 From: Gregory Owens <5419829+owensgl@users.noreply.github.com> Date: Wed, 10 Jan 2024 13:57:41 -0800 Subject: [PATCH] Update lab_1.md --- labs/lab_1.md | 28 +++++++++++++--------------- 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/labs/lab_1.md b/labs/lab_1.md index 582871f9c..7043330ba 100644 --- a/labs/lab_1.md +++ b/labs/lab_1.md @@ -4,8 +4,8 @@ element: lab layout: default --- -# Introduction -## objectives +# Section 1 +## Objectives - Describe key reasons for learning shell. - Navigate your file system using the command line. @@ -14,7 +14,7 @@ layout: default *** -## questions +## Questions - What is a command shell and why would I use one? - How can I move around on my computer? @@ -378,9 +378,7 @@ using the command line shell enables us to make our workflow more efficient and - Tab completion can reduce errors from mistyping and make work more efficient in the shell. *** - -# Navigating files and directories - +# Section 2 ## Objectives @@ -658,7 +656,8 @@ The commands `cd`, and `cd ~` are very useful for quickly navigating back to you *** -## objectives +# Section 3 +## Objectives - View, search within, copy, move, and rename files. Create new directories. - Use wildcards (`*`) to perform operations on multiple files. @@ -667,7 +666,7 @@ The commands `cd`, and `cd ~` are very useful for quickly navigating back to you *** -## questions +## Questions - How can I view and search file contents? - How can I create, copy and delete files and directories? @@ -734,7 +733,6 @@ each result starts with `/`. ## Challenge -## Exercise Do each of the following tasks from your current directory using a single `ls` command for each: @@ -753,7 +751,7 @@ what you need to solve the bonus problem. ## Challenge -## Exercise + `echo` is a built-in shell command that writes its arguments, like a line of text to standard output. The `echo` command can also be used with pattern matching characters, such as wildcard characters. @@ -818,7 +816,7 @@ For more information on advanced usage of `history`, read section 9.3 of ## Challenge -## Exercise + Find the line number in your history for the command that listed all the .sh files in `/usr/bin`. Rerun that command. @@ -856,7 +854,7 @@ $ cat bullkelp_001_R1.fastq -## Exercise +## Challenge 1. Print out the contents of the `~/shell_data/untrimmed_fastq/bullkelp_001_R1.fastq` file. What is the last line of the file? What command would only print the last lines of a file? @@ -908,7 +906,7 @@ forward to the next instance of this sequence motif. If you instead type `?` and return, you will search backwards and move up the file to previous examples of this motif. -## Exercise +## Challenge What are the next three nucleotides (characters) after the first instance of the sequence quoted above? @@ -1202,7 +1200,7 @@ you will be asked whether you want to override your permission settings. Be extr or with variables (covered later). A mistaken `rm` command can delete things you don't want to be deleted. -## Exercise +## Challenge Starting in the `shell_data/untrimmed_fastq/` directory, do the following: @@ -1215,7 +1213,7 @@ Starting in the `shell_data/untrimmed_fastq/` directory, do the following: *** -## keypoints +## Keypoints - You can view file contents using `less`, `cat`, `head` or `tail`. - The commands `cp`, `mv`, and `mkdir` are useful for manipulating existing files and creating new directories.