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README.md

Workshop Schedule

Day 1

Time Topic Instructor
9:30 - 10:10 Workshop introduction Radhika
10:10 - 11:40 Introduction to Shell Meeta/Will
11:40 - 12:00 Overview of self-learning materials and homework submission Will

Before the next class:

  1. Please study the contents and work through all the code within the following lessons:

NOTE: To run through the code above, you will need to be logged into the FAS-RC cluster and working on a compute node (i.e. your command prompt should have the word compute in it).

  1. Complete the exercises:
    • Each lesson above contain exercises; please go through each of them.
    • Copy over your the answers for the exercises into a plain text file on your local computer, using Notepad++, TextWrangler or similar.
      • Please do not copy all of the content from your Terminal, just the answers.
    • Upload the text file to Dropbox the day before the next class.

Questions?

  • If you get stuck due to an error while runnning code in the lesson, email us
  • Post any conceptual questions that you would like to have reviewed in class here.

Day 2

Time Topic Instructor
09:30 - 10:45 Self-learning lessons review Radhika/Will
10:45 - 12:00 Loops and automation Meeta

Before the next class:

  1. Please study the contents and work through all the code within the following lessons:

NOTE: To run through the code above, you will need to be logged into the FAS-RC cluster and working on a compute node (i.e. your command prompt should have the word compute in it).

  1. Complete the exercises:
    • Each lesson above contain exercises; please go through each of them.
    • Copy over your the answers for the exercises into a plain text file on your local computer, using Notepad++, TextWrangler or similar.
      • Please do not copy all of the content from your Terminal, just the answers.
    • Upload the text file to Dropbox the day before the next class.

Questions?

  • If you get stuck due to an error while runnning code in the lesson, email us
  • Post any conceptual questions that you would like to have reviewed in class here.

Day 3

Time Topic Instructor
09:30 - 10:00 Self-learning lessons review All
10:00 - 11:15 Introduction to the FAS-RC cluster Radhika
11:15 - 11:45 Exercise (answer key) Will
11:45 - 12:00 Wrap up Radhika

Dataset

Introduction to Shell: Dataset

Answer keys

Advanced bash commands

If you are interested in learning some more advanced tools for working on the command-line, we encourage you to walk-through the materials linked below:

Resources

Cheat sheets:

Online tutorials:

General help:

  • Google it! - if you don't know how to do something, try Googling it, other people have probably had the same question.
  • Learn by doing! There's no real other way to learn this than by trying it out.
    • Use vim on your laptop
    • Move around the directory structure on your laptop using the Terminal/Shell counts
    • Open folders and files using the command open
    • Automate something you don't really need to automate
  • Use man bash to get more information about bash (bourne-again shell)

These materials have been developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC). These are open access materials distributed under the terms of the Creative Commons Attribution license (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.