Tool for storing and debugging QIIME2 codes

Hi all,

I am wondering if there is a tool similar to Atom or Virtual Code Studio that is specific to QIIME2 codes. I know QIIME2 has been written in Python but it does not necessary follow Python rules so we cannot set Python for storing and debugging QIIME2 codes. Are there any tools available for this?

Hello Negin,

I’m not sure I understand your goal. Qiime 2 includes a artifact API written in Python.

Are you asking about debugging the Qiime 2 command line interface (q2cli)?

Are you asking about using a Jupyter Notebook to manage a series of Qiime 2 commands in a single document?


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I second @colinbrislawn’s suggestion of Jupyter notebooks. They have served me well for years.

I’ve also been playing with running qiime2 with the CLI-interface in snakemake. I particularly like it when I have multiple sequencing runs I want to combine, because then I just have to make a per-run manifest, and run a single command.



Yes, I mean for both debugging purposes and storing codes. So then debugging can happen if we set for Python in VS code or Jupyter Notebook then? Great!

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