Shell Genomics: Instructor Notes

This lesson will introduce learners to fundamental skills needed for working with their computers through a command-line interface (using
the bash shell). They will learn how to navigate their file system, computationally manipulate their files (e.g. copying, moving, renaming), search files, redirect output and write shell scripts. By the end of the lesson, learners will be prepared to move on to using more advanced bioinformatic command line tools (see the lesson on Data Wrangling and Processing). This lesson is meant to be taught in its entirety. For novice learners, schedule around 4 hours for this lesson. If your learners are
already somewhat familiar with the bash shell, the earlier episodes can be condensed. This lesson uses data hosted on an Amazon Machine Instance (AMI). Instructors will be sent information on how to log-in to the AMI by the workshop coordinator a few days before the workshop. If you are running a self-organized workshop, register the workshop with our self-organized workshop form and send us an email at with information on how many people you expect to have at the workshop, and we’ll start instances for you to use in the workshop. The day before the workshop, we’ll send you the login information for your learners. Learners will work through an Amazon Web Service (AWS) instance for this lesson. The workshop coordinator will set up AWS instances for
your workshop a few days ahead of time. Put the links for all instances on your workshop Etherpad and have learners put their name next
to the instance they will use. This prevents learners from accidentally messing up another learner’s filesystem. The workshop coordinator usually sets up more AWS instances than needed for the registered learners.
If a learner accidentally deletes or overwrites data files, you can have them change to a different AWS instance.

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