1 Introduction & Linux Server Accounts

Welcome to the first MICB 405 lab! Today, we’re going to get started with the essential skills and tools you’ll be using for the rest of the course.

Slides

You can download the slides for this tutorial below.

Logging in

Once you have followed the setup steps and have opened Command Prompt (Windows) or Terminal (macOS, Linux), you should be ready to log in!

Use the following command, replacing <username> with your actual username:

ssh <username>@orca1.bcgsc.ca

Enter your password when prompted. Don’t worry when characters don’t appear - this is an intentional security feature.

You may have to respond to additonal prompts by typing in an answer (such as yes) and pressing Enter.

Let’s break this command down: ssh is the command and stands for “secure shell”. It allows users to log on to remote (opposite of “local”, which is your computer in this instance) servers. All following text is the argument. There may be many arguments and each of these would be separated by spaces. <username> is mostly obvious, but crucially this positions your shell in the home directory of username on the server’s system with the correct permissions. If everyone were to log on as root (“Administrator” in Windows-speak) this would be bad. orca1.bcgsc.ca (everything after the @) is known as the hostname or domain name and is the name of the device on the network it is connected to. Super-nerds sometimes replace this with the IP address.

Bonus

Review the manual pages for ls, cd, and pwd by typing man followed by the command. Can you use them to move through your local machine’s folder system and find out where you are? How about the Orca server?

To exit the man page, press q.

Delve into man pages and help

1. What is the difference between the man page, and --help or -h argument added to a command? When would you use either option? (try it on some commands, or look through StackExchange if you’re confused)

2. Here is a list of Bash commands often used in bioinformatics. Look up the man page for at least one of them. What do you think they do? Hypothetically, in what way do you think they could be used in a bioinformatics context? Which arguments would be the most handy? Discuss within your group!

   1. grep
   2. tr
   3. awk

Terminal keyboard shortcuts

After typing some text, can you navigate, copy, and paste text without using the mouse? With some practice, this will be a lot faster.

Terminal keyboard shortcuts

keyboard	Action
tab	Autocomplete
↑ / ↓	Navigate command history backwards/forwards
ctrl + c	Kill process
ctrl + d	End terminal or ssh session (or use exit)
ctrl + r	Search command history
ctrl + a	Move to beginning of line
ctrl + e	Move to end of line
alt + b	Move back one word
alt + f	Move forward one word
ctrl + u	Cut/kill text before cursor
ctrl + k	Cut/kill text after cursor:
ctrl + y	Paste/yank (previously cut) text
ctrl + shift + -	Undo typing

Advanced

Create a new file by running nano testfile.txt in your home directory or on your local machine (Use ctrl + o to save and ctrl + x to exit nano).

Additonal resources

If you complete these tasks, check this page out for further reading and practice!!