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Dependency direction

GoliathOmics is a specialized application on the GoliathApp platform. It calls GoliathAlign and MethylExtractor as standalone utilities. The dependency edges point toward this repository.

flowchart BT
  omics["GoliathOmics"]
  app["GoliathApp"]
  align["GoliathAlign"]
  extract["MethylExtractor"]
  omics --> app
  omics --> align
  omics --> extract

GoliathOmics depends on the platform and on two utilities. Those three products do not depend on GoliathOmics.

Upstream What this product takes from it What that product contains about GoliathOmics
GoliathApp Gateway (methyl-gateway), engine DDL, RBAC, portal shell, claim and submit protocol, domain.compiler used to lower a DomainProgram No genomics seeds, handlers, or product types
GoliathAlign Pinned image and binaries for linear Mojo alignment and for methylGrapher Align / MethylCall / MergeCpG No reference to GoliathApp or GoliathOmics
MethylExtractor Pinned binary that writes per-chromosome HDF5 from a linear BAM No reference to GoliathApp or GoliathOmics

GoliathAlign and MethylExtractor also carry no reference to each other through this product. GoliathOmics chooses which utility runs for a sample. The WGBS pangenome path calls GoliathAlign for align and for extract. The linear and stock-pangenome paths call MethylExtractor after alignment. Required tool features are listed in omics-tool-requirements.md.

What stays in this repository

  • Science packages under packages/
  • DomainPrograms, profiles, analytes, and assay procedures under workflow_engine/domain/
  • Action handlers in workers/methyl_worker/
  • Database content the platform does not own: cfg.analyte, action-catalog and data-type seeds, reference-asset seeds, and the study pipelines
  • Release assemble and deploy scripts, deploy profiles, and the worker image bootstrap

The gateway process installed from a GoliathOmics release is the GoliathApp wheel. Its console script is methyl-gateway. goliath-gateway is the platform name for that service. This repository does not contain workflow_engine/rest/.

Names

methyl-* remains the genomics CLI alias for one release cycle (methyl-workflow-run, methyl-cfg, methyl-study-start). Platform commands use the goliath prefix and are documented with GoliathApp.

GOLIATH_ALIGN_ROOT points at a GoliathAlign checkout. MOJO_ALIGN_ROOT and a sibling directory named mojo-align remain one-cycle aliases. Older chapters that say MethylPipeline mean this product. Older chapters that say mojo-align mean GoliathAlign.

GoliathWorkflow is not a run path.