- [Voiceover] Hey there, welcome to the second video
in our three-part series
about installing the QIIME software,
using Virtual Box on a Windows computer.
In part one, we installed Virtual Box,
which is a software that lets you run,
sort of, a computer within your own computer.
If you are starting here and you haven't done that yet,
you can go watch our first video.
I'll make sure to put a link to it
down in the description of this one.
And if you wanna skip ahead,
say you've already done
most of the stuff we talk about here,
I'll also put a link to the third video.
So in this video, we're going to be downloading
the QIIME image from the website
and getting it set up.
If you go to qiime.org,
Q-I-I-M-E dot org.
Click on this QIIME Virtual Box link.
If you're coming right from the other video,
you probably already have this open somewhere.
Looking at these instructions,
we've finished number one.
Now it's time for number two.
Download the 64-bit QIIME Virtual Box,
which is over here in the Resources page.
Now I found this page a little confusing at first.
Mostly because I didn't know what to look for.
So I can tell you exactly where to go
and you won't have to deal with that.
The stuff up here,
is not what you're looking for.
These are, like, 16S tools.
Right now, we want this,
the latest QIIME Virtual Box image.
I'm going to right-click it.
Save it as.
I'm going to save it to my Documents folder.
If you have one of those unzipping tools like I do,
I have WinZip, but there's plenty of them out there,
that should be the type of file that it's saying this is.
It's a dot gz file.
In order to open it up, after it's done downloading,
you're going to have to unzip it.
I'm not going to show this part in the tutorial,
it's different for everyone,
if you're downloading something like this, to unzip a file,
whether it's for this one, or sometime in the future,
you want one of them, be very very careful
where you're actually downloading something from.
The websites that host file unzippers are full of spam,
ads and pretty nasty viruses.
Anyway, you are going to save this.
Okay, I've skipped ahead a little bit.
I have saved that program to my computer
and I've also unzipped it, using my unzipping tool.
If you are confused about how to get past that step,
you can leave a comment and I can walk you through it.
It's uh, it's not super complicated
and there's a lot of, there's just,
everyone has their own way that they like to do that so,
the way that I do it might not be
the way that you want to.
So I've unzipped that file. Now I have it.
It's a dot vbi file now.
Anyway, I have it downloaded into my Documents folder.
And I have another tip for you all actually,
which is, I've installed this,
I've done this whole process on,
I think, 18 computers now.
The first time, I downloaded it and unzipped it,
like normal, but all the times after that,
I actually put the unzipped file
onto an external hard drive
and then used that to transfer it
from computer to computer,
instead of downloading it everytime,
just because it's such a big file.
It's like 13 gigabytes unzipped.
And that was just faster honestly,
for me at least, with my internet connection.
So if you are planning on putting this
on a bunch of computers at once,
Virtual Box is small enough that you can probably
downloaded it on each one if you feel like it,
there's not a huge time difference,
but for the whole unzipping thing,
it's just easier to carry around the actual image file.
So the next thing that we're gonna do
is go back to our Virtual Box Manager here.
This looks pretty blank, pretty boring
but it's not going to pretty soon.
Click this New button.
This window might look a little bit different for you
depending on what version of Windows you have.
But they all have the same fields in it and everything.
You're gonna put in the name of your machine.
I actually already have a QIIME machine
on my computer but I'm making another one
for this tutorial so I'm gonna name this one,
QIIME2 over there.
And then I'm gonna go down to Type.
Press Linux.
And what should come up here is a Ubuntu 64-bit.
Now apparently there's a pretty common problem
that crops up here for people,
where they see Linux, they see Ubuntu,
but the only option they have is 32-bit.
I've never run into this issue
but I think they have a tutorial on how to fix it
on the QIIME website.
Either you have the wrong version of Virtual Box
because you might have downloaded
like, the 32-bit version of that,
or there's something up with your computer,
or your computer is just really old.
If your computer is a 32-bit computer,
I'm not sure this whole process is gonna work for you.
Sorry to tell you that now.
Anyway, click Ubuntu 64-bit,
if it doesn't come up automatically,
and press Next.
This memory size screen,
I know, sort of, you have this automatic desire
to just keep clicking Next
but you need to make sure that
the allotted RAM for this program
is more than 768 megabytes.
They say, on the website, that they need 1024 at least.
You know, I don't think there's,
I don't think there's any harm
in putting a little more in there.
And then we press Next.
So here, it's asking if you wanna make
a new computer within a computer,
or if you wanna use an existing one.
Well, we just downloaded an existing one.
So you're gonna click this third option down here.
And this folder icon on the right.
Choose a virtual hard disk file.
And navigate to the one that you just downloaded.
Mine is right here.
It should be a red box,
if you installed Virtual Box correctly,
and you know, checked all those boxes
about file extensions and stuff.
I told you to but you know, maybe you skipped that part.
Now you press Create.
And look at that, it's created.
Pretty straightforward.
So this tells you some of the specs
of your virtual machine.
And if you wanna get it started,
just press the Start button.
When you first start it,
for the very first time,
you're not gonna be able to make it super big.
See I can maximize this
but this screen is still pretty small.
You get to fix that later, I promise.
So this is all loaded now.
This is your virtual machine.
It's telling me
that I need to update something.
It says there's a 195 updates.
Well, we're not going to do that right now.
I'm in the middle of recording a tutorial,
that's very rude of you, computer.
So this desktop has loaded.
You've created this space.
Now you have to install QIIME
inside of this piece of computer.
So your screen should be looking something like this,
pretty blank, pretty boring.
It's, you know, it's a blank computer
that they've made for you.
The only thing on this is QIIME.
You're pretty much in the home stretch now
but I will warn you,
we're about to do some command line stuff
so it's gonna look a little more like,
like coding, and not so much like pressing Next buttons.
So be mentally prepared for that.
There's two more things I'm gonna in this video
and then the very last stuff,
I'm gonna save for the third video.
So, I want you to click Devices,
up here on the left, this dropdown menu,
go to the very bottom,
and it says Insert Guest Additions CD Image.
Basically, they have like a CD in this fake computer.
And it's asking if you want to install
the things off of the CD.
You do. Press Run.
Basically on this computer, we're logged in
as someone who doesn't have the full permissions.
So we're not logged in as an administrator
on this computer.
Or I guess we are
but we need to put in a password
every time we try and install something.
This password is gonna come up a lot
so maybe write it down.
It's just the word qiime, in all lower case letters.
I'll narrate it for you.
q-i-i-m-e.
That's the password.
Press authenticate.
Or you know, Enter, is what I pressed.
So basically, it's loading things
off of the fake CD.
Okay, when it says, "Press Return to close this window."
Press Enter or Return to close the window.
I love it when it gives you directions.
So this next stuff,
it does tell you on the QIIME website how to do this,
but for whatever reason,
I found it really hard to navigate.
I think other people do too,
which is why a bunch of students asked me
to make this tutorial for them.
So I'm just warning you, I'm gonna walk you
really step by step here.
I'm gonna go under the assumption
that you've never put anything
in a command line terminal before.
That this is completely new to you.
If it's not, I mean, I'm sorry.
You know, hopefully the sound of my voice
is soothing or something.
So the next thing that you're gonna do
is click this picture of a CD over here.
This is the CD you just installed.
I'm gonna drag this window over here.
I would suggest having this in full screen
instead of the tiny little computer box
that it sets up for you automatically,
especially now that we're gonna be
putting things into the terminal window.
This black box is the terminal window.
When you see this little tilde S,
that means it's waiting for you to put a command in.
So this purple box, it's called a terminal.
We're gonna be doing a few things in it.
It's not as scary as it looks.
Actually, for the purposes of this video,
we're just gonna be doing one thing in it.
It's called the pseudo-command.
Now, earlier you saw that popup
that asked if you were the super user
and asked for a password.
The pseudo-command is pretty much the same as
"Run as Administrator" in Windows.
You know, you have that little shield icon,
and it's asking if you want to run as an administrator.
That's the same thing that we're gonna do here.
Type in the letters S-U-D-O.
So basically the way that this interface works is
it's just typing.
You can't even click around at all.
It's just typing.
And the first thing you type in is the command.
Sometimes you put in a few letters
for clarifying the command
and then sometimes you put in like,
the name of a file.
Your terminal is actually like, inside of a folder.
And I'll get more into this later,
but basically, in the same way as if you're navigating
like this folder tree over here,
like if I were to click on this.
It would get me into that folder.
You do a similar thing in command line.
But you do it using code
and not clicking around.
Anyway, I found a neat trick that you can do.
After the pseudo-command, you have to put in
whatever it is you wanna run.
We want to run this over here,
VBoxLinuxAdditions.run.
Now, I could either type in
the entire file location of this.
Or I can use the command line thing
to navigate to this folder
and then type in that name.
Or here's a cool trick.
Grab it with your mouse,
drag it into there,
wow, look at that.
So I didn't have to do any of that.
I just, I just dragged it and dropped it.
Of course, if you want to type it all in,
you're welcome to.
If you were watching this,
you know, a few months from now,
you might have a different edition here.
You might have different numbers.
I know that the tutorial
that exists on Youtube already,
I tried to type in his exact numbers,
it just wasn't working because we had different versions.
You can't just press Enter yet,
you have to give rid of these little quotes,
or I guess they're apostrophes,
before and after the file name.
You can use the left and right arrow keys to navigate.
So I just got rid of the apostrophes
on either side of the file location
and I'm gonna press Enter.
Now it's asking for the password.
When I type in the password,
the letters aren't gonna show up.
I guess it's a security thing.
They don't even give you asterisks or anything.
So I'm typing
Q-I-I-M-E, Enter.
And now it's running.
Okay, here we go.
It looks like it's done.
QIIME at QIIME whatever tilde dollar sign,
means that's done.
I'm gonna x out of this.
There's one more thing.
Maybe you noticed
but there's two folders here on the desktop.
Actually older versions of QIIME have folders
and a few files that are like ReadMe files.
But this version just has two folders.
In the Before You Start folder,
it tells you, it's got a little text file
that tells you a little bit about
what version you have and how to install it.
Basically, it's got more information
than I'm telling you verbally right now.
You may find it interesting.
And the other folder is a shared folder.
If you open it, there's nothing in it right now.
That's because we haven't set it up yet.
So you're going to want to
shut down your Virtual Box computer.
Not your actual computer.
Go to this little sun,
off sign symbol in the top right.
Press Shut Down.
Are you sure? Yes, you're sure.
Okay, so it's not running anymore,
Right here, it says QIIME2.
That's mine. Yours probably just says QIIME.
It is powered off.
There's one more thing we're gonna do in this video.
I know it's getting a little long
but like I said, it's a long process
and you're in the home stretch.
You are so close to being done.
Scroll down in this panel on the right,
and go to Shared Folders.
Click the word, Shared Folders.
So there shouldn't be any yet.
There shouldn't be anything here,
except for the word, you know, Machine Folders.
But there shouldn't be any folder set up yet.
If you do this before you install all the other QIIME stuff,
sometimes it, like, breaks it.
It's really annoying.
You have to then delete it and redo it
so I would not do this step before the stuff we just did.
So you are going to press
this blue envelope button with a green cross on it.
Adds new shared folder.
The folder path, this can be whatever you want.
At NC State, we have it set going to the desktop
because it's mostly students doing classwork
that are using the computers,
but if you're using this for your own lab work and stuff,
I would make a dedicated folder.
Basically what this does is,
I don't know if you noticed
while you had your Virtual Box open,
but you don't have the same files in that
as you do on your regular computer.
In fact, right now, the only to get files there
is to upload them to the internet,
open up the internet inside the Virtual Box
and download them there.
Well, that's a pain.
So that's why they have this shared folder tool.
Basically it's like a little link
between your computer and the virtual computer.
So I have this going to the desktop.
You know, it doesn't really matter where it's going to
but what does matter is the folder name.
This is very important.
Give rid of whatever word is here already.
And type in,
Capital S, lowercase h,
a-r-e-d, underscore,
Capital F-o-l-d-e-r.
Shared Folder.
Capital first letters with an underscore in between.
It's got to be exactly that spelling.
Press OK.
And then press OK again.
It saved your settings.
It says you have a shared folder.
In order to check that the shared folder works,
start up your machine again.
I know. It takes a little while,
to start it up and then close it again.
It's kind of annoying.
While that's booting up,
I'm gonna show you something on my desktop.
So I have, besides a few programs on my desktop,
I have this picture called Untitled.
I made it just for you.
It says the word test image on it.
This is my test image.
This is to make sure that it actually works.
So if this shows up
in the shared folder in our Virtual Box,
that means they're successfully linked.
Okay, so as this is opened,
you should notice something different.
Do you know what it is?
If you look at the shared folder,
there's this little,
there's this little lock symbol on it,
in a white square.
That should mean
that it's successfully set up.
But we'll only know when we see my test image.
And look, there it is.
Double-click on this image.
Says test image, looks about right.
So now, if I put things on my desktop outside of this,
they'll show up here.
And vice versa, if I write something inside of this,
or have an image that I wanna save,
or you know, any other kind of file
that I wanna save to send to people,
I can just put it in the shared folder.
Sometimes it takes a while
to load in between.
Sometimes it takes so long that I've just restarted it.
I don't know if you're supposed to restart
every time you move files in between
if you want them to show up.
I haven't played around with this particular aspect
that much, but that's how you set it up
and it's obviously a pretty useful tool.
Okay, this concludes the second video tutorial
on using QIIME,
well, installing it, using Virtual Box.
Thanks for watching.
And make sure to tune in to the third video
where I show you how to finish up the process.
See ya.