I am working through chapter 3 of the q2book (3. An interactive introduction to QIIME 2 — q2book) and have been following along with the tutorial after activating my qiime environment (amplicon distribution). I have a question about this step:
"The next step is viewing this visualization. You can do this in a few ways, but the one I recommend right now is using QIIME 2 View. Open that page in your web browser now. You should see a big box on the screen where you can drop a QIIME 2 artifact or visualization to view it. Load the
demux.qzv visualization by dragging and dropping it onto that box. A QIIME 2 visualization should load. (**TODO: The user may not know how to locate a file they have generated on the command line. Point to some guidance on this.)"
I located the file using find ~/ -type f -name "demux.qzv" and was surprised to see it in my user folder /Users/eve//demux.qvz rather than in my qiime environment folder. I am curious as to why that is, and if there is a way to instead save visualizations into the qiime environment folder. For reference, this is how I downloaded the data (as described in the tutorial):
Great job locating the file! and good question, the reason the visualization is not in the environment folder is because the environment folder should only contain the packages necessary to run the qiime2 environment.
It is possible to save your outputs to your environment folder but there are many reasons this is not a good idea. One reason is that often environments need to be deleted completely. This is normal, they can stop working as they should and need to be reinstalled, or a new version is released that you will want to use instead. In such cases, you dont want your precious output data to be deleted as well!
You can think of the environment like hand which will make the changes to the data that you tell it to make, and those changes will be provided to you as an output. You are likely working in your users folder and that is why the output is going there, there is nothing wrong with this.
That said, you can make a folder somewhere (not in your env ) for the output files of the q2book tutorial to stay more organized.
Simply make a new folder named q2books_outputs (or what ever you want to name it ). Then when you run qiime commands specify the new folder path in the output (in this case it would be:
--o-visualization <your file path here>/demux.qza.
FYI, every qiime command the output is specified with
--o-<type of output>
I hope this makes sense! please let me know if you have any other questions.
That makes perfect sense, thank you for your thorough and helpful explanation