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GW-HIVE / CensuScope

CensuScope is designed and optimized for the quick detection of the components in a given NGS metagenomic dataset and provides users with a standard format report of components into species or higher taxonomic node resolution.
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Recreate CensuScope Via Python #1

Open HadleyKing opened 2 months ago

HadleyKing commented 2 months ago

Building on https://github.com/GW-HIVE/Platform/issues/92, CensuScope needs to be updated to a more modern framework. The current plan is to rebuild the PHP wrapper into a Python wrapper that is more accessible for current hardware.

HadleyKing commented 2 months ago

Refactoring the censuscope.php into the censu-scope.py is in progress.

cwoodside1278 commented 1 month ago

Not sure how to copy this over into the new HIVE-platform project? @HadleyKing @kee007ney

kee007ney commented 1 month ago

Note to self: we want to run CensuScope outside of the HIVE environment with the updated NT to test if this will resolve the issue of not being able to update NT.

Will be run as a Docker so it can be integrated into HIVE. NT will not be part of the Docker image.

Full TaxDB may be part of the image -- Hadley and I don't know how to make two Docker images talk to each other and it works as is, so given the speed requirement, we'll just have a 20Gb Docker image.

penningtonea commented 1 week ago

Need @HadleyKing upload local deployment documentation