LAMPrEY

LAMPrEY (Large-scale Automated Multi-level Proteomics Evaluation by Python) is a Docker-based quality control pipeline server for quantitative proteomics. It is designed for laboratories that want to organize proteomics pipelines, process RAW files automatically, and review QC results through a web interface.

Full documentation: LAMPrEY documentation

What It Provides

• project and pipeline management through the Django admin
• automated RAW file processing with MaxQuant and RawTools
• upload queue and per-run job management from the pipeline page
• an interactive QC dashboard with project, pipeline, and uploader filters
• an authenticated API for programmatic access

Requirements

• Docker Engine
• Docker Compose, either docker-compose or docker compose
• git-lfs
• make

For full installation details, fallback setup paths, and troubleshooting, see the Installation guide.

Quick Start

Assuming you have the above requirements installed, you can get started with LAMPrEY in a few steps:

git lfs install
git clone git@github.com:LewisResearchGroup/LAMPrEY.git LAMPrEY
cd LAMPrEY
git lfs pull
./scripts/generate_config.sh
make init
make devel   # development server on http://127.0.0.1:8000

Setup Modes

make init performs the first-time setup using the published container image:

• runs migrations
• prompts for a Django superuser
• collects static files
• bootstraps demo data

make init-local performs the same setup, but builds the image locally with docker-compose-develop.yml.

Common Commands

make devel         # start the development stack on http://127.0.0.1:8000
make devel-build   # rebuild and start the development stack
make serve         # start the production-style stack
make down          # stop containers
make test          # run tests

Notes

• Generated configuration is stored in .env.
• Local persistent data is stored under ./data/.
• The admin panel is available at /admin after startup.
• The dashboard is available at /dashboard after login.
• Pipeline uploads and API requests are scoped to the authenticated user's projects.
• The bundled MaxQuant ZIP is stored with Git LFS.
• If make or git-lfs is missing, or if you need the local-build fallback (make init-local), use the installation guide.
• For installation details, admin usage, API documentation, and operational notes, see the documentation site.