Move to using pungi for the sample and snakemake CLI management code.

rotary-genomics / rotary

Assembly/annotation workflow for Nanopore-based microbial genome data containing circular DNA elements

BSD 3-Clause "New" or "Revised" License

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Move to using pungi for the sample and snakemake CLI management code. #137

Closed LeeBergstrand closed 5 months ago

LeeBergstrand commented 5 months ago

Moved dataset.py, run.py, sample.py, and utils.py to pungi (https://github.com/rotary-genomics/pungi)
Import functionality from pungi
Update README.md install install instructions.

LeeBergstrand commented 5 months ago

@jmtsuji Once we add pungi to Conda, it should simplify the installation. For now, the only way to install it is manually. Once it's in conda or pip, we can add it to enviroment.yml, etc.

LeeBergstrand commented 5 months ago

@jmtsuji Passed my end-to-end tests.

LeeBergstrand commented 5 months ago

Great!