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Incompatible Biopython version in Ariba Docker image #317

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KuangXY3 opened this issue Nov 7, 2021 · 1 comment
Open

Incompatible Biopython version in Ariba Docker image #317

KuangXY3 opened this issue Nov 7, 2021 · 1 comment

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@KuangXY3
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KuangXY3 commented Nov 7, 2021

I got an error when running 'ariba getref ncbi out.ncbi' in Docker.
The error is:
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.
Should Ariba's Docker image contain compatible packages needed for running Ariba commands? Please help with this issue! Thanks!

@shenwei356
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Just install an old biopython before installing ariba.
pip install biopython==1.77
pip install ariba

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