Installing QIIME 2 for an undergraduate course

Hi, I am looking for a suggestion about the best way to install Qiime (v1 or v2 is fine) for a class I will be teaching. The students will be using their personal computers - some Mac, some PC and in some cases probably not the most robust machines - and will need to individually install the software, which I think will be challenging for some. Am I correct that installing through Miniconda might have the best chance of success? Thanks for any help!

Bill

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Hello Bill,

Yes, I recommend installing Qiime2 using Miniconda. Miniconda is also helpful for installing other computational biology software.

Colin

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Thanks Colin! That’s what I thought, but wanted to double check with an expert. It is nice to see a familiar face here in the forum after > 1 year since my last post!

Bill

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Thanks! Welcome back to the forums. :wave:

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Hi @wlandesman,

I’m with @colinbrislawn that I think a miniconda installation is the most robust.

But, if I can offer an alternative suggestion, you may want to consider a common login to a shared server or resource. It may be easier for students who have lower memory machines or struggle to install the virtual box/WLS to access the data, and it bypasses a lot of messy installation time. For workshops, the team here sets up an EC2 instance; I’m not sure if those are config files that could be used or adapted because I’ve never set one up, but someone else might be able to comment. If you have a local server, you could also potentially set up shared resources on that system. The advantage is that then you have shared files, less installation headaches and more equitable access to resources. The downside is that it takes time on your part and costs money to set up an EC2 server.

Best,
Justine

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Thanks for the suggestion! This sounds like a great solution to look into!

Bill

You can also contact the fine folk at Cyverse. See the following post:

I am sure they’d be happy to work with you on setting up QIIME 2 access for your students. Cyverse is free and I am sure they’d love to highlight your use case! Also, this will remove any issues with access to appropriate computing resources.

-Cheers!
-Mike

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Wow, thanks so much Mike. I will definitely look into that as well!

Bill

MARCH 6 UPDATE: Just wanted to follow up and say that this platform is working out very well for my class. All of my students can work with Qiime and different datasets without worrying about large uploads and processing speed. The Cyverse team has graciously guided me through the setup process and troubleshooting. Thanks again for the tip!

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