omnibioai-work

Runtime working directory for the OmniBioAI platform. This directory stores all artifacts, outputs, and intermediate files generated during workflow execution, tool runs, and analysis pipelines.

All contents are runtime-generated and excluded from version control via .gitignore. The directory structure is preserved via .gitkeep files.

Directory Structure

omnibioai-work/
├── runs/ # General tool and analysis runs (not tracked)
├── workflow_runner_runs/ # Workflow execution run outputs (not tracked)
├── workflow_runner_exec/ # Workflow execution working directories (not tracked)
├── fastq_qc_runs/ # FASTQ QC pipeline outputs (not tracked)
├── fastq_trimmer_runs/ # FASTQ trimmer pipeline outputs (not tracked)
├── pathway_enrichment_runs/ # Pathway enrichment analysis outputs (not tracked)
├── out/ # General output directory (not tracked)
├── storage/ # Persistent storage (not tracked)
├── object_storage/ # Object storage (not tracked)
├── objects/ # Runtime objects (not tracked)
├── videos/ # Video processing scratch space (not tracked)
├── backups/ # Destination for omnibioai-utils' scheduled backup scripts
│ ├── config/ # (not tracked)
│ ├── neo4j/ # (not tracked)
│ └── system-state/ # Daily output of backup-system-state.sh (.env,
│ # cloudflared, systemd, crontab) — see
│ # omnibioai-utils' README
└── object_registry.json # Object registry index

Setup

This directory is referenced in the OmniBioAI docker-compose stack via the WORK_DIR environment variable:

WORK_DIR=/home/manish/Desktop/machine/omnibioai-work

It is mounted into multiple services:

volumes:
- ${WORK_DIR}/runs:/app/work/runs
- ${WORK_DIR}/objects:/app/work/objects
- ${WORK_DIR}/workflow_runner_exec:/app/work/workflow_runner_exec
- ${WORK_DIR}/workflow_runner_runs:/app/work/workflow_runner_runs
- ${WORK_DIR}/pathway_enrichment_runs:/app/work/pathway_enrichment_runs

On first run after cloning, execute the setup script to recreate all required directories:

bash setup.sh

Cleaning Up

To clear all runtime artifacts and start fresh:

bash cleanup.sh

Warning: This will permanently delete all run outputs, workflow results, and stored objects.

Related Repositories

• omnibioai — main Django workbench application
• omnibioai-tes — task execution service that writes to runs/
• omnibioai-workflow-bundles — workflows that write to workflow_runner_runs/
• omnibioai-data — input data directory
• omnibioai-utils — backup-system-state.sh writes into backups/system-state/