How some-earth-2514/gnps_local works
GNPS Local is a single-user, offline metabolomics analysis application. A researcher uploads MS/MS spectra and, for FBMN, a feature-quantification table through the local API; the runner manages jobs and executes workflow code that produces molecular networks and library annotations. The tree also documents molecular networking, GC-MS processing, and library conversion capabilities. Workflow wiring beyond the sampled API and excerpts is inferred from names and the README, so uncertain internal processing links are omitted.
Main entry points: orchestrator.py Job manager · app.py HTTP API · fbmn.py FBMN · molecular_networking.py Molecular networking
Components 13
Local interface
- HTTP API
local_runner/app.py
Job execution
- Job manager
local_runner/orchestrator.py - Job files
local_runner/orchestrator.py
Analysis workflows
- FBMN
local_runner/workflows/fbmn.py - Molecular networking
local_runner/workflows/molecular_networking.py - Molecular networking (MCN)
local_runner/workflows/mcn.py - GC-MS workflow
local_runner/workflows/mshub_gc.py - Library annotations
local_runner/workflows/getGNPS_library_annotations_local.py
Supporting capabilities
- FBMN processing
feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts - Network outputs
metabolomics-snets-v2/tools/metabolomicsnetsv2/scripts - Library conversion
library_conversion/tools/library_conversion/bin - GC-MS processing
mshub-gc/tools/mshub-gc/proc
Other components
- Researcher
Connections 15
- Researcher → HTTP API: submits data
- HTTP API → Job manager: submits jobs
- HTTP API → Job manager: queries status
- Job manager → Job files: stores job data
- Job manager → FBMN: dispatches FBMN
- Job manager → Molecular networking: dispatches workflow
- Job manager → Molecular networking (MCN): dispatches workflow
- Job manager → GC-MS workflow: dispatches workflow
- Job manager → Library annotations: dispatches workflow
- FBMN → FBMN processing: uses processing
- GC-MS workflow → GC-MS processing: uses processing
- Molecular networking → Network outputs: uses networking tools
- Molecular networking (MCN) → Network outputs: uses networking tools
- Library annotations → Library conversion: optional conversion
- Job manager → HTTP API: returns job results