Queue Generation System

Generate sample queues with QC injections for mass spectrometry instruments (XCalibur, Chronos, Hystar).

▶ Try the live demos

Launch the queue generator in your browser →

Launch the config editor in your browser →

No install, no account. The queue generator demo lets you upload a CSV/XLSX sample table (or load a bundled example), pick the instrument / sampler / pattern, preview the queue, and download it. The config editor demo lets you inspect, edit, and validate the configuration in the browser.

qg is a standalone tool: upload a CSV/XLSX sample table in the GUI (or pass a parameters JSON to the CLI), configure the queue, preview, and download — no FGCZ/B-Fabric required. It also runs as the FGCZ B-Fabric portal app (LIMS order browsing + workunit upload); see the B-Fabric guide.

📖 Documentation: fgcz.github.io/qg — local-app and editor guides, the queue-generation algorithm, and the configuration reference.

Installation

pip install ms-qg              # as a dependency
uv sync --no-group portal      # for development in this repo, B-Fabric-free

Requires Python 3.13 or newer.

This installs the local app plus the qg, qg-assign-positions, and qg-validate CLIs. The core install has no bfabric, fastapi, starlette, or python-gitlab dependency — import qg, the local app, and the CLIs all work without them. For the FGCZ B-Fabric portal, install the ms-qg[bfabric] extra — see the B-Fabric guide.

Quick Start

Local app — no B-Fabric

make app-local
# or: qg-app-local
# or: uv run marimo run src/qg/apps/queue_app_local.py

Upload a sample table — ready-made examples (vial/plate, single- and multi-project) live in docs/examples/ — pick the instrument / sampler / pattern, preview, and download the queue plus its parameters JSON. See docs/users/local_app.md.

CLI

uv run qg config.json -o queue.csv   # generate a queue from a parameters JSON (stdout if no -o)
uv run qg-assign-positions config.json -o positioned.json  # assign/validate physical positions only
uv run qg-validate                   # validate the config files

Running at FGCZ? The B-Fabric portal app, its ms-qg[bfabric] install, project cache seeding, and deployment all live in the B-Fabric guide.

Supported Configurations

Technologies

• Proteomics
• Metabolomics (with pos/neg polarity)
• Lipidomics (with pos/neg polarity)

Samplers

Output Formats

• XCalibur (.csv, xcalibur / xcalibur_sii)
• Chronos (.csv)
• Hystar (.xml)

Queue Parameters JSON

Queue generation takes a JSON file with a parameters object (instrument, sampler, output format, pattern, …) and a nested queue object (batches plus samples, or plates/cells for plate input). The canonical schema and field-by-field reference live in one place: docs/reference/config.md.

Example Output

File Name,Path,Instrument Method,Position,Inj Vol,Sample Type,Sample Name
20260112_001_C37180_autoQC02dia,D:\Data2San\p37180\Proteomics\ASTRAL_1\cpanse_20260112,C:\Methods\Proteomics\ASTRAL_1\DIA_60min.meth,B:F8,1.0,QC,autoQC02dia
20260112_002_C37180_autoQC01,D:\Data2San\p37180\Proteomics\ASTRAL_1\cpanse_20260112,C:\Methods\Proteomics\ASTRAL_1\DIA_60min.meth,B:F9,2.0,QC,autoQC01
20260112_003_C37180_S852285_HeLa_10ng,D:\Data2San\p37180\Proteomics\ASTRAL_1\cpanse_20260112,C:\Methods\Proteomics\ASTRAL_1\DIA_60min.meth,Y:A1,2.0,Unknown,HeLa_10ng

Configuration Files

Static config lives in qg_configs/, grouped under core/{structure,position,formatting,methods}/ and ui/. The per-file reference (purpose, columns, examples) is maintained in one place: docs/reference/config.md.