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franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
https://franciscozorrilla.github.io/metaGEM/
MIT License
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'compositionVis' , 'abundanceVis' and 'taxonomyVis' rule errors #48

Closed shreyanshumale closed 3 years ago

shreyanshumale commented 3 years ago

Hello Francisco!

  1. I was following the unseenbio examples, but when I run: bash metaGEM.sh -t compositionVis the terminal throws an error that there is no task under that name. When I check the Snakefile, I do find a compositionVis rule.
  2. And when I run bash metaGEM.sh -t taxonomyVis. I get this error: No rule to produce taxonomyVis
  3. Same error as 2 again when I run bash command for abundanceVis

Can you please tell me why this happens?

Thanks, Shreyansh

franciscozorrilla commented 3 years ago

Hi Shreyan,

Ah yes sorry about that, many of the visualization rules are still being developed and I need to add them to the metaGEM.sh parser. Also the plotting scripts are generally very basic at the moment and are mostly meant for sanity checking. Let me know if there are any particular result visualizations that you would find useful. In any case, I have added this item to the to-do list for the next release of metaGEM v1.1.0.

Best wishes, Francisco

franciscozorrilla commented 3 years ago

fixed in issue #63