DE-LIMP/docker-compose.yml at main · bsphinney/DE-LIMP · GitHub

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# =============================================================================
# docker-compose.yml — Run DE-LIMP with embedded DIA-NN search
# =============================================================================
#
# Prerequisites:
#   1. Build DIA-NN image first:
#      bash build_diann_docker.sh          (Mac/Linux)
#      .\build_diann_docker.ps1            (Windows PowerShell)
#
#   2. Create data directory:
#      mkdir -p data/raw data/fasta data/output
#
# Usage:
#   docker compose up                      (start DE-LIMP)
#   docker compose up --build              (rebuild after code changes)
#   docker compose down                    (stop)
#
# Then open: http://localhost:3838
#
# Place your files:
#   data/raw/       ← .d / .raw / .mzML files
#   data/fasta/     ← .fasta files
#   data/output/    ← DIA-NN results appear here
#   data/ssh/       ← SSH key for HPC search (e.g., id_ed25519)
# =============================================================================

services:
  delimp:
    build:
      context: .
      dockerfile: Dockerfile.search
    ports:
      - "3838:3838"
    volumes:
      - ./data:/data
    environment:
      - DELIMP_DATA_DIR=/data
      - DELIMP_SSH_USER=${DELIMP_SSH_USER:-}
      - DELIMP_SSH_KEY=${DELIMP_SSH_KEY:-}