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geneontology / pipeline

Declarative pipeline for the Gene Ontology.
https://build.geneontology.org/job/geneontology/job/pipeline/
BSD 3-Clause "New" or "Revised" License
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The ontology build process must point to pipeline resources #162

Open kltm opened 4 years ago

kltm commented 4 years ago

We probably want to do a general audit, but the go-ontology build process is depending on inputs from the old pipeline (!).

In general, all external resources that are GO products that are referenced by the ontology build process must be changed to point to the current (internal pipeline) version of that resource.

For example: https://github.com/geneontology/go-ontology/blob/79299ea5aafdd1fad735c9bf3bcbf86a77c2a044/src/ontology/Makefile#L151-L155 The best "general" location of this file it going to be http://snapshot.geneontology.org/metadata/db-xrefs.legacy or http://current.geneontology.org/metadata/db-xrefs.legacy . That said, if this is running in the pipeline, the URL needs to be something like http://skyhook.berkeleyboip.org/A/SERIES/OF_RESOLVED_VARIABLES/metadata/db-xrefs.legacy .

kltm commented 4 years ago

Once https://github.com/geneontology/go-ontology/issues/18870 is clear, we can add the necessary runtime variables.