First off: Thanks for developing QIIME!
I have a few questions and points regarding headless use of QIIME.
For the last two years I’ve been using QIIME1 and I have only dabbled superficially with QIIME2 a couple of months ago. While the new features are great, one thing that has put me off, was the move from log-files to interactive outputs.
I understand this move should enable less-computing-literate scientists to analyse data. However, I found, though this might just be my very personal case at my university, that it is easier for me to get access to HPC, than setup QIIME on a VM or server where I can run it interactively in a notebook. Installation via
conda commands also seemed to be quite straightforward.
Yet, on HPC this high level of interactivity makes data processing less convenient. I have to copy outputs and have to have another local installation of QIIME to inspect the output.
Is there a plan to make a more HPC/headless-friendly version of QIIME2?
Originally I’ve asked a question about running QIIME1 headlessly:
is there a flag that could be set during QIIME installation to configure it for headless use? Or are there flags to run certain scripts/programmes headlessly?
I’ve now come across a Thermokrast’s post here, which sheds a little light as to why
matplotlib is configured the way it is.
matplotlib default config varies from installation to installation, it depends on what libraries are available at install time (e.g. qt). Some environments (such as an academic HPC) might have their own matplotlib configs, so we generally steer clear from forcing all of our users to use our config for third party tools. The example I linked to above recommends using Agg as the backend, but there might be other users out there who prefer to use a different offscreen render (or a custom render even!). Similarly, matplotlib also supports per-project configs, which we also don’t want to interfere with. Anyway, we will support some form of general QIIME 2 config in the future — perhaps it is worth continuing this discussion then, to see if there is some way for us to provide a fallback config for tools like matplotlib. Thanks!
Would be possible to set the
DISPLAY configuration with flags during installation or for individual scripts?