macOS Catalina and QIIME

Has anyone had trouble with installing QIIME2 on a Mac running Catalina? The new OS system removed QIIME1.9 from my system as a security threat. :slight_smile:
Cheers
Becks

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Hi @BecksHawaii,

No issue with QIIME 2, but I haven’t tried a QIIME 1 installation in over 12 months. It’s been deprecated for at least 18, so it might just be time to move over and fully embrace QIIME 2?

Best,
Justine

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Hello Becks,

I’m having the exact same problems too as I also have Catalina OSX and the system refuses to download the program. I’m trying to work through it and I’m wondering if you ever came by a solution.

Cheers,
Veronica

Welcome to the forum @veronica_rodriguez!

Just to clarify: you cannot download QIIME 2 on Catalina? Or QIIME 1?

Since QIIME 1 is no longer maintained, there is unlikely to be a solution if Catalina does not like QIIME 1.

I’m trying to download QIIME2 on Catalina natively with miniconda

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Thanks for clarifying and giving the install details! (it sounded like @BecksHawaii’s problem was qiime1, so just wanted to make sure)

We will attempt to replicate. Could you please provide the error message you are receiving and more specific system info? Thanks!

A friend of mine recently did this (recently like 1-2 months ago). She told me it was a bit of an arduous process to get QIIME1 and QIIME2 running again. I will ask her some of those details.

I did invite her to come onto the forum, but she hasn’t accepted yet. Ben

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So, my friend told me:

This was the website the worked for QIIME1:
http://www.metagenomics.wiki/tools/16s/qiime/install/packagesnotfounderror

Apparently to get QIIME2 to run, she had to re-install everything into a new Python Environment. She stressed that when she installed it, she had to create a new environment separate from the one that QIIME1 was installed in (this makes sense to me).

She also stressed that nay plug-ins that you use will have to be installed in the new environment as well (e.g., Songbird etc.). ’

Her ultimate recommendation though, she told me not to update to Catalina. Sorry if you have already.

Ben

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You should be running a QIIME 1.9.1 environment separately from any of your QIIME 2 environments: the requirements are totally different and they won’t work together. This is one of the benefits and drawbacks of conda: you can have multiple environments, like multiple rooms in your house. We might have a sink in your laundry room, kitchen, bathroom1 and bathroom2 but they’re different versions of the base release “sink” which slightly different behavior. Like, my kitchen sink is slightly more feature complete because the head pops off. (However, this is Europe so its not entirely feature complete. I miss my garbage disposal.) Environments can take on slightly different features/behaviors, and its important to keep them self contained and separate.

Best,
Justine

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I hear you, I didn’t know exactly which part or why she installed it in conflcting/overlapping environments. I wasn’t present when she installed it so I can only assume there was some issue regarding when and how she installed QIIME1 and QIIME2.

Although, to her benefit, she is quite good w/ conda and I may be understating the issues she encountered.

Ben

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Sorry, I don’t mean to be difficult :slight_smile: . Environment management can be hard and it’s been a weird week for it here. I apologize if I came off as condescending or just rude.

Best,
Justine

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