Resurrect and migrate to Snakemake

ebi-gene-expression-group / anatomical-systems-mapping

Atlas metadata and ontology mappings

MIT License

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Resurrect and migrate to Snakemake #4

Closed pcm32 closed 2 years ago

pcm32 commented 2 years ago

This PR

Migrates the workflow from make to Snakemake, so that it can run in the cluster with proper dependency resolution
Fixes Scala and shell issues seen on runtime.
Move dependencies to depend on a container atlas-metadata-base hosted on quay.io (defined in atlas-containers repo).

pmb59 commented 2 years ago

Why the main Snakefile has extension .smk? If this was intended, this file should be specified in the run command excitedly with -s:

By default, Snakemake will search for 'Snakefile', 'snakefile', 'workflow/Snakefile', 'workflow/snakefile' beneath the current working directory, in this order. Only if you definitely want a different layout, you need to use this parameter.

pcm32 commented 2 years ago

Working from Jenkins, so will merge.