Finish Unix/Bash Series

[cjsifuen]

This is meant to be a hands-on tutorial for learning Unix structure and bash shell skills.

Introduction to the Unix file system:

• Log in to a Unix-based system using your terminal
• Understand the concept of a file system and the basic file system structure in Unix (e.g. /, /home, /usr, /bin, etc.)
• List the contents of a directory using the ls command
• Change directories using the cd command
• Create a new directory using the mkdir command
• Remove a file or directory using the rm command

Basic file operations:

• Display the contents of a file using the cat command
• Display the contents of a file one page at a time using the less command
• Copy a file from one location to another using the cp command
• Move a file from one location to another using the mv command

Advanced file operations:

• Use wildcard characters to match multiple files (e.g. *, ?, [])
• Use command line options to modify the behavior of commands (e.g. -l for ls, -r for cp)
• Search for text within files using the grep command
• Sort the contents of a file using the sort command
• Join the contents of two files based on common columns using the join command

Writing and executing shell scripts:

• Create a new shell script using a text editor (e.g. nano, vi)
• Make the script executable using the chmod command
• Execute the script using the ./ command
• Pass command line arguments to the script
• Use conditional statements (if, then, else) and loops (for, while) in your script

Bioinformatics examples:

• Download a FASTA file of a protein sequence from a database (e.g. UniProt)
• Count the number of occurrences of a specific amino acid in the sequence using grep and wc
• Search for all possible restriction enzyme sites in the sequence using grep
• Extract all the gene sequences from a GenBank file using grep
• Use awk to calculate the average GC content of the sequences in a FASTA file
• Use a shell script to automate the analysis of multiple FASTA files in a directory

By the end of this tutorial, attendees should have a solid understanding of the Unix file system, the basics of the Bash shell, and how to use these skills to solve simple bioinformatics problems. As people continue to work in the field, they may find that they need to learn additional skills and tools, but this tutorial should provide a good foundation to build upon.

[cjsifuen]

After replanning, I think the following should work as an outline. I will mark off the topics as I go along.

Session 1

Installation and Resources

• [x] Download and install bash (Windows)
• [x] Download and install data

Introducing the Shell

• [x] What is the shell?
• [x] Why use the shell? This can be a simple thought experiment.

Using the Shell

• [x] Open terminal -- for mac and windows os
• [x] Interact through the use of commands -- example with cal
• [x] Command syntax and modifications -- modify the use of cal
• [x] Example of broken down commands
• [x] Getting --help with commands, and using man
• [x] Dealing with errors

Introduction to the file system

• [x] What is the File System -- A series of parent-child directories
• [x] Image of GUI vs CL
• [x] Absolute and Relative Paths
• [x] Finding where we are with pwd
• [x] Viewing files withls, including additional flags and hidden items
• [x] Changing directories within the system with cd
• [x] Making directories with mkdir
• [x] Copying files with cp
• [x] Moving and renaming items with mv
• [x] Removing files and directories with rm

Session 2

Basic and Advanced File Interactions

• cat, head, tail, grep
• cut, join
• variables, set/unset, env
• saving and redirecting
• curl/wget
• glob
• wc and sort; unique

Putting it together

• piping and scripting
• chmod
• passing CL arguments
• if/else and loops
• workflow