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thomasgurry / amplicon_sequencing_pipeline

Pipeline for computing OTU tables from 16S or ITS amplicon sequencing data.
MIT License
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ImportError: No module named biom #1

Open HuangRuocheng opened 6 years ago

HuangRuocheng commented 6 years ago

Dear Developers,

I'm trying this pipeline. However, when I typed 

python ./scripts/Master.py -h

, it turned out:

Traceback (most recent call last):
  File "./scripts/Master.py", line 18, in <module>
    import QualityControl as QC
  File ".../amplicon_sequencing_pipeline/scripts/QualityControl.py", line 17, in <module>
    import Formatting as frmt
  File ".../amplicon_sequencing_pipeline/scripts/Formatting.py", line 13, in <module>
    import biom
ImportError: No module named biom

I'm using Python 2.7.10, and I can't find package biom online or in this pipeline.

Could you give a help? Thanks very much!

Huang Ruocheng

cduvallet commented 6 years ago

Hello! Thanks for raising this.

You can get the biom module here: http://biom-format.org/

That said, I don't think the pipeline actually uses biom format in any of the default functions - it's only included as optional functions in the Formatting.py module (to convert traditional text file OTU tables into biom format). So if you're having a hard time installing it, I'm pretty sure you can comment out the import calls in Formatting.py without breaking anything...

Because we mostly use this pipeline on our in-house clusters, we haven't given much instruction for installation. Apologies in advance for difficulties here - installing this pipeline is something we know may be difficult, and will hopefully get a chance to simplify someday!