omnibioai-data

Runtime data directory for the OmniBioAI platform. This repository contains the directory structure, sample files, and registry configuration needed to bootstrap a local OmniBioAI instance.

Large runtime files (datasets, uploads, results, cached data, tool images) are excluded from version control via .gitignore. The directory structure is preserved via .gitkeep files.

Directory Structure

omnibioai-data/
├── datasets/               # User datasets (not tracked)
├── downloads/              # Downloaded files (not tracked)
├── uploads/                # User uploads (not tracked)
├── results/                # Analysis results (not tracked)
├── reports/                # Generated reports (not tracked)
├── logs/                   # Application logs (not tracked)
├── cache/                  # Cached data (not tracked)
├── igv_snapshots/          # IGV genome browser snapshots (not tracked)
├── single_cell/            # Single-cell analysis data (not tracked)
├── omni_object_storage/    # OmniBioAI object storage (not tracked)
├── omni_objects/           # OmniBioAI objects (not tracked)
├── objects/                # Runtime objects (not tracked)
├── PubMed/                 # PubMed cache (not tracked)
├── reference/              # Reference genomes/annotations (not tracked)
├── tool-images/            # Tool container images (not tracked)
├── omnibioai-tool-images/  # OmniBioAI tool images (not tracked)
├── local_registry/         # Local model/tool registry (not tracked)
├── object_registry.json    # Object registry index
├── workflow_registry.json  # Workflow registry index
└── sample files            # Sample data files for testing

Sample Files

Small sample files are included for testing and development:

File	Description
sample1.csv	Sample expression matrix
sample2.csv	Sample expression matrix
sample1_normalize.csv	Normalized expression matrix
sample2_normalize.csv	Normalized expression matrix
sample_annotations.gff3	Sample genome annotations (GFF3)
sample_annotations.tsv	Sample annotations (TSV)
sample_regions.bed	Sample genomic regions (BED)
sample_sequences.fasta	Sample sequences (FASTA)

Setup

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

DATA_DIR=/home/manish/Desktop/machine/omnibioai-data

On first run, create the required runtime directories:

mkdir -p datasets downloads uploads results reports logs cache \
         igv_snapshots single_cell omni_object_storage omni_objects \
         objects PubMed reference tool-images omnibioai-tool-images \
         local_registry

Related Repositories

• omnibioai — main Django workbench application
• omnibioai-tes — task execution service
• omnibioai-tool-images — tool container image definitions
• omnibioai-db-init — database initialization scripts