running QIIME headlessly (DISPLAY)

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Michael Baron

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Jan 15, 2018, 5:00:14 AM1/15/18
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Hello everybody,

I know support has been suspended, but I feel QIIME2 is even more difficult for a headless system, considering you need to view every output with a separate command, which requires a DISPLAY to be set.

I've come across various threads now where one would have to edit the `matplotlibrc`, changing to backend from `qt4agg` to `agg`. Or using export MPLBACKEND="Agg".

However, 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?

Thanks!
Michael

Colin Brislawn

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Jan 15, 2018, 2:37:02 PM1/15/18
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Hello Michael,

This is a great question. I think you can ask the Qiime developers directly over in this section on the Qiime 2 forums: https://forum.qiime2.org/c/dev-discussion 

I'm willing to bet that more than half of the qiime devs use Qiime on headless clusters. Let's see what they suggest. 

Colin

Michael Baron

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Jan 16, 2018, 3:52:50 AM1/16/18
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Hi Colin,

Probably a good idea to ask over there :)

Thanks,
Michael
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