How do I start the tutorial for QIIME2?

Hi all,
I am new to QIIME. I am trying to start the tutorials, but it isn't working. The link for the tutorial (per QIIME 2 website) is:

http://nbviewer.jupyter.org/github/biocore/qiime/blob/1.9.1/examples/ipynb/illumina_overview_tutorial.ipynb .

Please refer to this link to see what I am talking, as it might make a whole lot more sense.

On this page it says that the tutorial has to be downloaded. There is text that appears to be a command, but it does not say where to type this command. I assumed this command should be typed in the terminal window of the QIIME2 machine in virtual box (I have the latest update installed). I interpret the "in []" to mean type this command in brackets. I copied/pasted the command in brackets, even again not in brackets. I've repeated this a few time, each time getting the same result:

bash: !tar: event not found.

I assume this is python lingo for "it didn't work."

I am attempting to upload a screen shot for further clarification, but my screenshot file only appears like text to me.. I don't know if this works, hopefully you can see it after I post this.

How do I download this tutorial? Is this command supposed to be entered elsewhere?

Thank you for any help, I appreciate it. I have never even done coding before, so I'm asking for any answers to have limited technical jargon.

Thank you again,
Dan

1 Like

Hi @walsh0311!

Welcome to the forum! We’re here to help!

These are actually tutorials for QIIME 1.9, you can find the tutorials for QIIME 2 at docs.qiime2.org.

If you use those, I suspect you’ll have a lot more success. :slight_smile:

Thanks for the screenshot! It looks like you have a good installation!


Bonus Info:

Since you are new to this I wanted to explain a bit what is going on with your example:

You were copying and pasting commands from an IPython notebook. It’s a nice way to run Python code interactively (letting you run a little bit of code and then seeing what happens), but it’s also convenient to run “shell” or “bash” commands in. Because the Python language never uses the ! character, IPython decided that any line of code that starts with that, it will treat as a shell command.

Unfortunately, when actually running in bash (your terminal in the screenshot), the ! does have a meaning which results in errors like you observed:

If you just remove the ! you will be able to run the tar command. Which is a program that you can usually find in bash environments like the one you have.

In QIIME 2, we put all of our commands behind a single qiime command. This way there’s only ever 1 program that bash has to find instead of hundreds. It also makes it easy to tell when you are working with QIIME 1 or QIIME 2.

QIIME 1 will look something like this: some_kind_of_action.py -i whatever
whereas QIIME 2 will look like this: qiime some kind-of-action --i-thing whatever

Hope that gives some background, good luck with your analysis!

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An off-topic reply has been split into a new topic: Importing error

Please keep replies on-topic in the future.

Good luck, welcome to your deep dive! Try to run the commands without the “!” preceding wget / tar. Ben

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