Move to snakemake #23
Open
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This project started out using the experimental "shark" build system, which never reached maturity, and at some point I moved it to using a shell script to run the pipeline. That worked for ad-hoc use, as I could comment out bits I didn't need to run, but as we want to make this more of a CI ran metric for the IUCN team, it needs something more appropriate. To that end I've migrated to using Snakemake, a popular Python data-science pipeline running tool.
This PR: