Installing Qiime on Google Colab

Can you create an instruction on how to setup Qiime on Google Colab? I found this fantastic tutorial from Gibbons Lab. Because I don’t know how I often this tutorial will be maintained, I borrowed their setup file and created my own Google Colab setup (see the ipbynb file attached).

It would be nice if something like this can be attached on the Qiime website and be maintained. qiime setup.zip (4.1 KB)

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Thanks for the suggestion, @Evil_Puppy! I don’t think we have any Google Colab experts on the team, perhaps @seangibbons (I’m assuming this is the same Gibbons Lab referenced above) would be interested in contributing a Community Tutorial here on the forum? Thanks!

:qiime2:

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I’m looping in @cdiener who put together that Colab tutorial :slight_smile:

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Hi,

The script on Github is maintained. For instance, I just pushed fixes a few days ago.

So running the following in colab should be enough:

!wget https://github.com/Gibbons-Lab/isb_course_2020/raw/master/setup_qiime2.py
%run setup_qiime2.py

I do think it is a good idea to port it to its own repository to make it easier to use and more maintainable.

This should work in general with the exception of plugins in the Python interface (things like from qiime2.plugins import feature_table won’t work since the notebook runs Python 3.7). Plugins will work in the command line interface though.

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