When initially building the container, building the gemmi wheel fails, it appeared to be an issue to do with the C compiler and there have been some changes to this since gemmi V6 - see docs
Finally, snakemake depends on pulp. When running the cli command to process the model pdb files, this error occurred:
AttributeError: module 'pulp' has no attribute 'list_solvers
'list_solvers' is an addition in pulp v2.8, so i specified v2.7 in the req.txt file.
This is a general issue with snakemake itself and is an open issue on their repository.
I hope this is helpful information. If you would like to ask me anything else, please don't hesitate.
Hello, the docker container does not build successfully. I did get it all working by updating the requirements.txt files as follows:
api/requirements.txt
Fastapi depends on pydantic. I had to specify an earlier version, because since pydantic v2, 'model_' is now a protected namespace.
cli/requirements.txt
When initially building the container, building the gemmi wheel fails, it appeared to be an issue to do with the C compiler and there have been some changes to this since gemmi V6 - see docs
Finally, snakemake depends on pulp. When running the cli command to process the model pdb files, this error occurred:
AttributeError: module 'pulp' has no attribute 'list_solvers'list_solvers' is an addition in pulp v2.8, so i specified v2.7 in the req.txt file.
This is a general issue with snakemake itself and is an open issue on their repository.
I hope this is helpful information. If you would like to ask me anything else, please don't hesitate.