Goals of the lab

Most of the software applications that we use throughout the course will be command-line tools. The goal of this lab is to make sure that you are all familar with the basic commands used to navigate a unix command line.

Tutorials

We'll be using an excellent tutorial by Michael Stonebank -- http://info.ee.surrey.ac.uk/Teaching/Unix/

Specifically, I recommend:

  1. the introduction,
  2. tutorials one,
  3. tutorial two, and
  4. sections 5.1 and 5.2 of tutorial 5,

Remote access tutorial

Some of the analyses that we do will be run on clusters of computers (rather than the imacs in the lab). Becoming comfortable working on a remote machine is not too difficult, and is a valuable skill. The two most common tasks are logging in (typically accomplished using ssh) and copying files back and forth (usually done with scp). Fortunately, scp uses basically the same syntax as the cp command that occurs in the previous tutorial.

Text editor

We will need to use text editors (rather than word processors) for modifying the files that we use throughout the course. I highly recommend that you become comfortable with at least one good text editor.

For Mac

  1. BBEdit,
  2. its free version TextWrangler, or
  3. TextMate
are all good choices.

For Windows

  1. NotePad++
is a good, free editor.

For any platform

  1. jEdit
is a good, free editor.

test_execute.py script

After you are comfortable, then try running the test_execute.py script from a couple of different locations.

First you'll need to download the file from github, and save it on the machine that you are working on.

Try passing in files as arguments. Try launching it, opening a new Terminal window and killing the test_execute.py process (the executable that is running is listed as Python or python).