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biocore / qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
GNU General Public License v2.0
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set Agg backend in compute_core_microbiome.py and plot_semivariogram.py #1115

Closed jairideout closed 11 years ago

jairideout commented 11 years ago

In scripts/compute_core_microbiome.py and scripts/plot_semivariogram.py, the following two lines should be added at the top of the import statements (before the pylab imports):

from matplotlib import use
use('Agg', warn=False)

This is what other plotting scripts in QIIME currently do.

If these lines aren't present and a user's matplotlib install tries to load up a graphical backend without having a DISPLAY, the script will error out.

jairideout commented 11 years ago

Just verified with a user that adding these lines to the scripts will fix the error.

josenavas commented 11 years ago

Yes, I faced this problem developing some code and this line will fix it (I didn't noticed that there were not added to compute_core_microbiome.py)

cleme commented 11 years ago

@josenavas please don't fix this yet, I want a student of ours to fix this one as it would be a good way for him to get started with github.

josenavas commented 11 years ago

Great :)

jairideout commented 11 years ago

@charudatta-navare assigning this issue to you.