# Adventures with Unix in Windows 10
*Author: Chissa Rivaldi
Last Updated: 08/27/2018*
[Link to personal website](https://sites.nd.edu/crivaldi/)
[Link to Intro to Biocomputing tutorial slides from Week 1 Friday](https://docs.google.com/presentation/d/1fK_Y_O_ZVYCWAWh6EXcYmKqcyoP-_EVsrhtOqt6M8cQ/edit?usp=sharing)
---
## Why do we want a terminal on Windows?
Many times you'll run into software that can't run on 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](https://medium.freecodecamp.org/a-beginner-friendly-introduction-to-containers-vms-and-docker-79a9e3e119b), which is like putting a mini computer on your computer. These are *really useful* for [some workflows](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4567039/) but they're sort of clunky and we don't really need them to accomplish our current objective of simply getting started in UNIX.
---
#### To install, 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 figure 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.)
- Native install of Ubuntu
- Need Windows 10 with 2017 Fall Creator's Update or later - [Windows update page](https://support.microsoft.com/en-gb/help/4028685/windows-10-get-the-update)
- [Installation Instructions](https://tutorials.ubuntu.com/tutorial/tutorial-ubuntu-on-windows#0) - [Another Option](https://docs.microsoft.com/en-us/windows/wsl/install-win10)
- MobaXterm ([Website](https://mobaxterm.mobatek.net/download-home-edition.html))
- [Installation Instructions](https://blog.jez.io/2014/09/28/setting-up-mobaxterm-for-ssh-on-windows/) - Choose Home Edition
- In my experience, MobaXterm has more bells and whistles, but the tradeoff is that it's a bit slower to load.
- Cygwin - [Website](http://www.cygwin.com/)
- Pretty quick and light, make sure you install the tools you might want to use within a terminal (nano, git, python2, curl, wget, unzip, make, and openssh are the ones I chose as per [the class instructions](https://github.com/joneslabND/ICB_Fall2018)).
To test out your install, type
```ls```
and hit "Enter". What we're trying to do is get a **list** of the files in the directory (what you used to call a folder before you started your terminal).
A screen like this means you were almost certainly successful:
What you're seeing is an empty directory - there are no files here. This isn't necessarily bad - we'll make some files very soon!
### But I already have a ton of files on my computer - why can't we 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 if they can help it). 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.
$~$
$~$
$~$
$~$
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](https://www.howtogeek.com/261383/how-to-access-your-ubuntu-bash-files-in-windows-and-your-windows-system-drive-in-bash/)
$~$
---
$~$
### Note About Permissions
Some of you have a 'permission denied' error which comes up as you start exploring your windows directory (i.e. where your Documents, Desktop, etc. files are). The reason this is happening gets pretty complicated and has to do with the way the linux subsystem is built to work with Windows. We can get around this temporarily by using the command 'sudo' in front of the command you're trying to use.
For example, if you get something like this:
```
criva@Bistromath ~ ls Desktop
criva:'Permission Denied'
```
Then try 'sudo':
```
criva@Bistromath ~ sudo ls Desktop
Files/ Schedule/ Homework/
Paper1.pdf Rewrite.pdf
```
Which temporarily gives you administration privleges. It is important to not that you generally want to only use 'sudo' when you're absolutely sure you know what you want to do and how to do it, but for the commands we're using in this class we aren't going to be able to do too much damage. Be warned if you try to edit something deep in your Windows file system, you could very quickly destabalize your operating system.
#### Another option:
Run your terminal in Windows as an administrator. Using Ubuntu as an example, hit your windows key, then start typing 'Ubuntu' - you should see something like this:
When that pops up, don't press enter, but right click on the ubuntu icon and when the menu pops up, select 'Run as Administrator' - you should see something like this:
When you click that, a new terminal should open, ask to make changes to your computer (say yes) and then you *should* have your permission denied problems cease. Remember that there is not recycle bin when you're in a terminal - once you delete something it's gone forever, so proceed with caution when you're working as an admin.
$~$
---
$~$
### Other Tips
- Explainshell.com 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. https://jvns.ca/ (cool example: https://jvns.ca/zines/#linux-comics)
- 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:
- [Sublime](https://www.sublimetext.com/3)
- [Atom](https://atom.io/)
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