The sapporo-service is a standard implementation of the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification. WES provides a standardized way to submit, monitor, and retrieve results from computational workflows across different platforms.
The service builds on GA4GH WES 1.1.0 with additional capabilities defined in the sapporo-wes-2.1.0 specification, including output file downloads, RO-Crate metadata generation, run deletion, and JWT authentication. Each workflow engine runs inside its own Docker container, so the service does not require any engine-specific installation.
docker compose -f compose.docker.yml up -d
curl localhost:1122/service-infoSee the Getting Started guide for a complete walkthrough including workflow submission.
Deploying on the DDBJ/NIG supercomputer? See Deployment (NIG) for the
podman-compose+ Slurm REST API setup.
Full documentation is available at https://sapporo-wes.github.io/sapporo-service/.
- Getting Started - First-time tutorial: start the service, submit a workflow, retrieve results
- Installation - Install with pip or Docker, volume mount configuration
- Configuration - CLI options, environment variables, executable workflows
- WES Compatibility - GA4GH WES 1.1.0 and sapporo-wes 2.x compatibility matrix
- Authentication - JWT authentication, sapporo/external mode
- Architecture - run.sh abstraction, run directory, SQLite, RO-Crate, code structure
- RO-Crate - RO-Crate metadata generation specification
- Development - Development environment, testing, release process
- Deployment (NIG) - DDBJ/NIG supercomputer deployment with podman-compose and Slurm REST API
- Agent Skill - LLM/agent reference: submit workflows, poll status, retrieve outputs via
curl - Agent Quick Reference - Essential 4 commands in ~40 lines
This project is licensed under the Apache-2.0 license. See the LICENSE file for details.