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$ make_emperor.py -i ~/qiime_illumina_test/cdout/bdiv_even1114/weighted_unifrac_pc.txt -o ~/qiime_illumina_test/cdout/bdiv_even1114/weighted_unifrac_emperor_pcoa_plot -m map.tsv --custom_axes DaysSinceExperimentStart
 
$ make_emperor.py -i ~/qiime_illumina_test/cdout/bdiv_even1114/unweighted_unifrac_pc.txt -o ~/qiime_illumina_test/cdout/bdiv_even1114/unweighted_unifrac_emperor_pcoa_plot -m map.tsv --custom_axes DaysSinceExperimentStart 
Info

If you want to run the Qiime 1.9.1 on Atmosphere with Jupyter notebook you can do so using this protocol - QIIME-1.9.1 Using Atmosphere on Jupyter Notebook