Principles and Applications of Modern DNA Sequencing


Session 1: Introduction to computational genomics

Today's topics:

An introduction to Codio, the
Command Line, and Jupyter

Why do we use codio?

- Everything runs in the cloud.
- You do not need to worry about installing any software.
- You can run your assignments on *any* computer.

What could go wrong?

- If you completely screw up an assignment you must
ask us to reset your unit for you.

Open up a new terminal in Codio.

Hierarchical File System

Always know where you are and where your files are.

  # The root (top) of the entire filesystem (used for writing full paths).
  $ /

  # Here, in my current directory (used for writing relative paths).
  $ ./

  # Up one directory from my current directory (a relative path).
  $ ../

Hierarchical File System

Always know where you are and where your files are.

  # show the files and folders in a location (default target is cur dir)
  $ ls 

  # show result as a list for cur dir.
  $ ls -l ./

  # show another location on the filesystem
  $ ls -l /bin/

  # move to a new location. This becomes your new cur dir.
  $ cd folder/

Your location (current directory) starts from / (the root) and is described by a nested set of directory names leading to your location.

  # use 'pwd' program with no option or target to ask where am I now?
  $ pwd

We can make new directories and change our location.

  # make a new directory (mkdir is the program, genomics is the target)
  $ mkdir genomics

  # change directory (move) into the new directory and run pwd again
  $ cd genomics
  $ pwd

Learning bash command line tools

There are many great tutorials, and google always has an answer. If you have no background in using the terminal then you should complete the Linux Command Line Tutorial on Codio, listed under the Courses tab on the left.