Adventures with Unix in Windows 10

Author: Chissa Rivaldi Last Updated: 07/13/2019 Link to Intro to Biocomputing tutorial slides from Week 1 Friday

Why do we want a terminal on Windows?

Many times you’ll run into software that aren’t written for Windows. Sometimes your files are too big for your own computer. In these instances, you essentially need a new machine to do your work. You can install something called a virtual machine, which is like putting a mini computer on your computer. These are really useful for some workflows but they can easily take up a huge amount of space and we don’t really need them to accomplish our current objective of simply getting started in UNIX. There are tools like Binder and Docker that can be built for specific workflows and make reproducing workflows a breeze, but to get a command line on your local machine, we can get started with something less intensive.

First, figure out if you have a 32 or 64 bit operating system.

Press the windows key and type “about” - select the ‘About your PC’ option that comes up & look for ‘System type’ (see example below).

Now you can decide out which Unix setup you want to install. 32-bit users, you want Cygwin or MobaXterm. 64-bit users, you can either do a native install of Bash/Ubuntu or install either Cygwin or MobaXterm. (There are other options, but these are the ones I’ve had the most experience using/installing.)

To test out your install, type ls and hit “Enter”. This command prints list of the files in the directory (a.k.a. foler) you’re currently working in.

A screen like this means you were almost certainly successful:

What you’re seeing in this image is an empty directory - there are no files in this directory yet. You might have some, depending on where you started.

But I know I have a ton of files on my computer - why can’t I see them?

When you start playing with files on your own computer, you’ll notice that the file directory setup you’re using isn’t the one you’re used to (familiar directories like ‘Downloads’ or ‘Desktop’ will not be visible). This is because of the way that Unix and Windows interact (i.e. not at all). The way to access your files depends on whether you’re using native Ubuntu on Windows or Cygwin or MobaXterm and requires a working knowledge of file paths to understand what’s really going on.


Instructions for All Terminals

If you type cd with no arguments and hit “Enter”, you’ll always go to your default home folder. You can always find out what directory you are currently in by using the command pwd: $~$

This is similar to what your directory looks like now with a Cygwin setup (bonus: this was the exercise we did in class on Monday!). Some files/directories omitted for clarity. You want to go from your “Default Home” to your “Windows Home” - signified by the blue stars. To get there in this example, you need to go up two directories, then down four; see the red arrows. $~$ $~$ file paths $~$ $~$

You can do this all in one step. Here is what that command looks like on my computer (my username is ‘criva’):

For a Cygwin setup

criva@Bistromath ~ cd ../../cygdrive/c/Users/criva

or, alternatively, I could start anywhere on my file system and get to my Windows Home like this:

crivaldi@Bistromath ~ cd /cygdrive/c/Users/criva

The difference between these two commands is that in the first, you’re using a relative file path, and in the second, you’re using an absolute file path. The Software Carpentry lesson on file paths explains this thoroughly if you’d like this broken down in detail.


For Ubuntu on Windows setup

Relative path: cd ../../mnt/c/criva or absolute path: /mnt/c/criva

More info on Ubuntu in Windows 10



Other Tips

  • is really helpful when you’re learning commands (I still use it every now and then tbh)
  • Amazing blog with a lot of comic strip-like information about unix commands. (cool example:
  • If, at any point, you need to name something, do not use spaces. You can use: ‘_’ or ‘-‘ but keep it simple until we learn more about special characters. - Use PuTTy, CyberDuck, Rstudio to transport files back and forth (in command line, use the command scp is too tricky). - Good text editors with a graphical user interface (GUI) & some fancy tricks: