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AWS/Unix Review for Microbiome Analysis 2024
Workshop Pages for Students
AWS and Unix intro
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Connecting and properly using a cloud computing cluster at the CBW

by Jose Hector Galvez, Zhibin Lu & Rob Syme

Schedule:

Today's schedule can be found here.

Contents:

  1. Logging into AWS

  2. Introduction to the command line

    2.1 Exercise: Exploring the filesystem

  3. File manipulation

    3.1 Exercise: Reading text files

    3.3 Exercise: Editing text files

  4. Searching and sorting files

  5. Putting it all together

1. Logging into AWS

Description of the lab:

This section will show students how to login to AWS.

Slides (pdf)

You can find the instructions here.

2. Introduction to the command line

Description of the lab:

This section will show students the basics of the command line, with a focus on navigation.

Exercise: Exploring the filesystem

  1. Connect to your AWS instance

  2. Type the ls command - what is the output?

Solution 

$ ls
CourseData  R  workspace

The ls command lists the contents of a working directory.

  1. Type the pwd command - what is the output?
Solution 
$ pwd
/home/ubuntu

The pwd command shows the absolute path to the working directorpwy.

3. File manipulation

Description of the lab:

This section will show students how to manipulate files, including reading, editing, and renaming text files.

Additional material:

Here are two cheat-sheets that can be useful to have as a reference for common UNIX/Linux commands:

Exercise: Reading text files

Using the commands you just learned, explore the .gff file in your home directory.

  1. Is the file a text file?
Solution

Yes. You can use less, cat, head, or tail and get human-readable info. Note that this doesn't have anything to do with its file extension.

  1. How many lines does the file have?
Solution 
$ wc -l GCF_009858895.2_ASM985889v3_genomic.gff 
67 GCF_009858895.2_ASM985889v3_genomic.gff

There are 67 lines in this file.

  1. Can you read the content of the file using less?
Solution 
$ less GCF_009858895.2_ASM985889v3_genomic.gff

Exercise: Editing text files

Using the commands you just learned, create a file called helloworld.txt and edit it using nano.

  1. Write “Hello world” into the file. Save the file and exit nano.

  2. Create a subdirectory called “test”; move the helloworld.txt file into test.

  3. Create a copy of the helloworld.txt file called helloworld2.txt

  4. First, use the nano command to open a file called helloworld.txt

Solution 
$ nano helloworld.txt

Inside the nano editor, write "Hello world", then use the ^O option to write the changes and ^X to exit.

  1. Create a subdirectory called “test”; move the helloworld.txt file into test.
Solution

First, use the command mkdir to create this new directory. Then, use mv to move helloworld.txt into this directory.

$ mkdir test
$ mv helloworld.txt test/
  1. Create a copy of the helloworld.txt file called helloworld2.txt.
Solution

First, change the working directory using cd, then use the cp command to create the copy.

$ cd test
$ cp helloworld.txt helloworld2.txt

4. Searching and sorting files

Description of the lab:

This section will show students how to search for and in files.

Workshop notes and quiz questions here.

5. Putting it all together

Description of the lab:

This section will show students how the basic concepts fit together and how they apply in the context of bioinformatics.

Workshop notes and quiz questions here.