Use integrated package managment

sunbeam-labs / sbx_report

Generates a final report, with figures, from a Sunbeam run

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Use integrated package managment #10

Closed eclarke closed 5 years ago

eclarke commented 5 years ago

We should rewrite the rules to use their own conda environments, as the dependencies here may conflict with other extensions.

https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#integrated-package-management

ressy commented 5 years ago

Just made a pull request that I think should cover this one. (It's a simpler situation than the related sbx_kaiju issue since there's just one self-contained rule and no need to interact with the software inside the isolated environment.)