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sanger-pathogens / ariba

Antimicrobial Resistance Identification By Assembly
http://sanger-pathogens.github.io/ariba/
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Incompatible Biopython version in Ariba Docker image #317

Open KuangXY3 opened 2 years ago

KuangXY3 commented 2 years ago

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 commented 3 months ago

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