LAMPrEY

LAMPrEY 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: LewisResearchGroup.github.io/ProteomicsQC

What It Provides

• project and pipeline management through the Django admin
• automated RAW file processing with MaxQuant and RawTools
• an interactive QC dashboard
• an authenticated API for programmatic access

Requirements

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

Quick Start

Clone the repository:

git lfs install
git clone git@github.com:LewisResearchGroup/ProteomicsQC.git ProteomicsQC
cd ProteomicsQC
git lfs pull

The repository stores the bundled MaxQuant executable ZIP with Git LFS. Install git-lfs before cloning so app/seed/defaults/maxquant/MaxQuant_v_2.4.12.0.zip is downloaded as a real file instead of a small pointer.

If you download the repository from the GitHub web UI instead of cloning it, make sure the repository is configured to include Git LFS objects in archives. Otherwise the archive will contain only the LFS pointer file.

Generate the local configuration:

./scripts/generate_config.sh

Run the first-time setup:

make init

By default, make init uses the published container image.

If the published image is unavailable, use the local-build fallback:

make init-local

Start the application:

make devel   # development server on http://127.0.0.1:8000
make serve   # production-style server on http://localhost:8080

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
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 bundled MaxQuant ZIP is stored with Git LFS.
• For installation details, admin usage, API documentation, and operational notes, see the documentation site.