New GO pipeline. For context, see:

• geneontology#209

Overview

• Gathers external contributed files (GAFs, GPADs, ...)
  • The locations of these are stored in yaml metadata files
  • Groups can provide GAF or GPAD+GPI
• Performs filtering and checking
  • We use an adapted version of "Mike's script", see util/
  • Afterwards runs owltools checks and inferences
• Generates filtered files and derived files
  • GPAD, GAF and GPI
  • RDF for direct loading into blazegraph

Jenkins Job

Note these are not in production

• https://build.berkeleybop.org/job/go-gaf-release-snapshot
  • excludes ttl, excludes goa_uniprot_all, runs daily
• https://build.berkeleybop.org/job/go-gaf-release-production
  • excludes ttl, runs weekly
• https://build.berkeleybop.org/job/go-gaf-release-experimental
  • includes ttl

Everything is driven by a makefile. It should be possible to run the makefile locally, on an amazon machine slaved to jenkins, etc

Environment

The pipeline/environment.sh script can be used to setup the environment before the makefile is run. Use source to run the script:

source environment.sh

or

. environment.sh

Status

Note yet active. Running in parallel.