Open multiple .qzv files on Qiime2 view at once

I’m currently working on a dataset with many metadata variables, so I end up with many qzv files after running beta-analyses and other analyses on the dataset. When viewing them on Qiime2 view, I have to drag them in one at a time, return to the main site after I’m done with the file, and go through the same thing again for the next file. Looking around online, I couldn’t find any way to open them all on Qiime2 view at once. Is there a way to do this?


I have exactly the same problem. It is difficult to analyse all the data when you have numerous .qzv files and you need constantly jump between windows. I would like to know if there is any workaround or solution that can make it easier.
Right now I am redrawing some figures in a way I can compare then. But I like the process itself, it is an exercise for me to learn python


Hello @michael-nakai!

Unfortunately not :frowning:. You can also view QIIME 2 visualizations locally by running qiime tools view FILE.qzv, which could be scripted to open several files at once. Supporting “datasets” (including opening multiple visualizations) is definitely on our radar, stay tuned!


Hi @thermokarst

Thanks for the reply, makes sense! Unfortunately I’m currently using Qiime2 through Windows Subsystem for Linux (WSL) and am getting the “visualization view is currently not supported in headless environments” error (since WSL can’t launch Chrome on my windows through the Linux environment). Hope there’s a way to sidestep this in the future!

Yeah, that makes sense, @michael-nakai.

Three options

  • Check out this really old side-project that I whipped up a few years back: I just pulled down the files (for macOS) and they still work, so maybe you could modify or script this out a bit (feel free to fork the code)
  • You could use a VM for scripting calls to q2cli’s built-in viewer (suggested behind the scenes by @ChrisKeefe) , although that might be too much overhead for what you’re after here.
  • Investigate some kind of macro-recording tool, for automating browser clicks etc.



Thanks for all the help @thermokarst. I’ll probably try whipping up something in selenium for python to automate the drag/drop process, but I’ll look into that qzv-view you linked (looks like a fun side project!).

Again, thanks!

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