Refactor how CMash is called

nlapier2 / Metalign

Metalign: efficient alignment-based metagenomic profiling via containment min hash

MIT License

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Refactor how CMash is called #27

Closed dkoslicki closed 4 years ago

dkoslicki commented 4 years ago

Currently, CMash is being called via relative imports. Since the goal is to migrate to conda, it would be nice if the code just called CMash by looking at the $PATH (or wherever it's been installed). This will head off issues with planned re-structuring of the CMash repo.

nlapier2 commented 4 years ago

The recent update has done this for minimap2, KMC, and CMash.