docker-compose.yml

services:
  param:
    build:
      args: 
        http_proxy: ${http_proxy}
        https_proxy: ${https_proxy}
        no_proxy: ${no_proxy}
      dockerfile: Dockerfile.protein-prediction
    command: conda run -n alphafold2 --no-capture-output python extract_params.py --input /dataset/params/params_${MODEL}.npz --output_dir /output/weights/extracted/${MODEL}
    environment: 
      - DATASET_DIR=${DATASET_DIR}
      - EXPERIMENT_NAME=${EXPERIMENT_NAME}
      - MODEL=${MODEL}
      - OUTPUT_DIR=${OUTPUT_DIR}
      - http_proxy=${http_proxy}
      - https_proxy=${https_proxy}
      - no_proxy=${no_proxy}
    image: ${FINAL_IMAGE_NAME}:inference-ubuntu-20.04
    privileged: true
    volumes: 
      - ${DATASET_DIR}:/dataset
      - $PWD:/workspace
      - ${OUTPUT_DIR}:/output
    working_dir: /workspace/protein-prediction/models/aidd/pytorch/alphafold2/inference
  protein-prediction-preproc:
    build:
      args: 
        http_proxy: ${http_proxy}
        https_proxy: ${https_proxy}
        no_proxy: ${no_proxy}
      dockerfile: Dockerfile.protein-prediction
    command: conda run -n alphafold2 --no-capture-output bash online_preproc_baremetal.sh /output /dataset /output/samples /output/experiments/${EXPERIMENT_NAME}
    depends_on:
      param:
        condition: service_completed_successfully
    environment: 
      - DATASET_DIR=${DATASET_DIR}
      - EXPERIMENT_NAME=${EXPERIMENT_NAME}
      - MODEL=${MODEL}
      - OUTPUT_DIR=${OUTPUT_DIR}
      - http_proxy=${http_proxy}
      - https_proxy=${https_proxy}
      - no_proxy=${no_proxy}
    image: ${FINAL_IMAGE_NAME}:inference-ubuntu-20.04
    privileged: true
    volumes: 
      - ${DATASET_DIR}:/dataset
      - $PWD:/workspace
      - ${OUTPUT_DIR}:/output
    working_dir: /workspace/protein-prediction/quickstart/aidd/pytorch/alphafold2/inference
  protein-prediction-inference:
    build:
      args: 
        http_proxy: ${http_proxy}
        https_proxy: ${https_proxy}
        no_proxy: ${no_proxy}
      dockerfile: Dockerfile.protein-prediction
    command: conda run -n alphafold2 --no-capture-output bash online_inference_baremetal.sh /opt/conda/envs/alphafold2 /output /dataset /output/samples /output/experiments/${EXPERIMENT_NAME} ${MODEL}  
    depends_on:
      protein-prediction-preproc:
        condition: service_completed_successfully
    environment: 
      - DATASET_DIR=${DATASET_DIR}
      - EXPERIMENT_NAME=${EXPERIMENT_NAME}
      - MODEL=${MODEL}
      - OUTPUT_DIR=${OUTPUT_DIR}
      - http_proxy=${http_proxy}
      - https_proxy=${https_proxy}
      - no_proxy=${no_proxy}
    image: ${FINAL_IMAGE_NAME}:inference-ubuntu-20.04
    privileged: true
    volumes: 
      - ${DATASET_DIR}:/dataset
      - $PWD:/workspace
      - ${OUTPUT_DIR}:/output
    working_dir: /workspace/protein-prediction/quickstart/aidd/pytorch/alphafold2/inference