Workshop1.md

Workshop 1. (2nd March 2021). Introduction to computational biology, command line, Linux.

1.1. The workshop

• Piotr - background, interests, and bioinformatics experience
• Workshop participants - background, interests, experience, expectations
• What the workshop is about
  • Unofficial, informal - but a bit of a pilot for a future more systematic Comp Biol training at INoŚ
  • Goal: teach you something useful. I assume you want to learn.
  • Contents and pace flexible, I'll adjust to your needs and interests.
  • You don't need to attend individual classes. Drop any time. No grades or evaluations.
  • When teaching new stuff I assume you are comfortable with the previously taught stuff. Make sure you are!  

1.2. Bioinformatics and command line

• Bioinformatics vs. computational biology
  • Either way, we want to learn tools that are applicable to many data types, allow to simplify time-intensive tasks, and enable tackling projects on an otherwise-implausible scale
  • Mastering a set of relatively simple tools that we will be able to combine, mix-and-match --- to achieve exactly what you want with the data.
  • Learning it takes effort - but once you have it, you will have a set of scaleable, highly replicable tools that you will be able to reuse and modify for an ever-increasing set of tasks.
  • Understanding your data and knowing what you want is going to be the key, but once we have that, we should be able to do whatever :)
• Why use command line?
  • Less intuitive than pointing and clicking (Graphical User Interface - GUI), takes dedicated effort to learn
  • But more versatile, less platform-specific
  • Makes it easy to save and replicate sequences of operations
  • Makes it easy to keep the log of operations and repeat them, perhaps on new files
  • Makes it easy to run operations on many files at once
  • Many useful tools only exists in command-line mode
  • It's much easier to write your own scripts with a command-line-only interface
  • Computing clusters usually use command line... you need to know it if you work with big dats!
• Getting set up!
  • Software is platform-specific: Windows vs Mac vs Linux
  • Installing useful tools (Appendix 1 in the Book!): powerful text editor (Notepad++, BBEdit, or some of the alternatives!) and access to Unix/Linux command line
  • Setting up accounts on the cluster, connecting  

1.3. Unix/Linux - intro to the environment

• Basic vocab:
  • Shell - command interpretor in your Unix/Linux operating system. Allows you to interact with the computer.
  • Kernel - the central part of a Unix operating system, the core interface between a computer's hardware and the processes
  • Bash - a Unix shell and command language, default login shell for most Linux distributions
  • Terminal - that's where shell runs!
  • Shell session is the current state/environment in the shell/terminal, delimited by login/logout.
  • Prompt - the active line where you type commands. Often includes useful info - user name, current directory
• pwd --- where are you?
• The Linux file system - more vocab:
  • root - the superuser account, but also, the very bottom of the file structure
  • Directories, files
  • Path
  • Current/working directory
  • Home directory (~)
• ls --- listing directory contents
  • pointing at directories that you want listed!
  • arguments: -l, -h, -a ...
• getting help about commands!
  • man
  • --help, -h
  • Google :)
• cd --- changing directories
  • absolute vs relative path!

cd Project1
cd ..
cd ./Project1/Dataset1
cd /home/username/Project1/Dataset1
cd ../Dataset2
cd  / cd ~
cd -

• Effective navigation
  • up and down arrows move you to previously applied commands that you can now edit
  • command history lists previously
  • Ctrl+A, Ctrl+E - jump to the beginning/end of the edited command
  • Tab - autocompletes the command being typed
• mkdir --- making directories
• rmdir --- removing EMPTY directories
• touch --- as a way of making empty files
• mv --- change name or move
  • path as an extension of a filename!
  • keep attention to syntax!
  • relative vs. absolute path

mv OldName.txt NewName.txt
mv OldName.txt ../NewLocationAndName.txt
mv OldPath/OldName.txt ~/NewName.txt

• cp --- copy file to a new location. Perhaps under a new name!
  • cp -r --- copy recursively, the whole directory/file structure
  • what are other possible arguments?

cp MyFile.txt ~/Project1/
cp Project1/MyFile.txt MyFileRenamed.txt
cp -r Project1 Project1_copy

• rm --- removing files. Dangerous - there is no "Undo", no "Trash"!
• Wildcards: "*" for any string of characters, "?" for a single character. Great for moving/coping multiple files

cp ./* NewDirectory/
mv Sample123_R?.fastq ~/Project1/ReadsForSample123/

• Comments - text after #!

ls     # This command lists the contents of the directory!
rm *   # Be very careful! Are you sure this is what you want to do?

• exit - exiting your session!  

1.4. The HOMEWORK :)

• Read Chapter 1 and Chapter 4 in the book - recap what we have covered today!
• Practice! Follow the exercises in the book, make sure you are comfortable with all material covered.
• Make sure that you have accounts on one of the INoŚ clusters! I recommend azor.
• Send me a brief summary/example of the type of computational biology tasks that would be useful to you!
• Read Chapter 5 in the book. During the next session, we will mostly be covering its contents.