docker-compose.yml

# Docker compose to run the docker image lluisb3/mask3d (non-root image)#
# Create image running docker-build-script.sh to create user with same ID as hosr user #
# IMPORTANT to create directories in volumes on the host machine with user ownership before running #

services:
  hlung:
    image: lluisb3/hlung:${TAG}
    volumes:
      - ${INPUT_PATH_WSI}:/home/user/app/data/tcga/wsi/TCGA-18-3417-01Z-00-DX1.tif
      - ${INPUT_PATH_PATCHES}:/home/user/app/data/tcga/patches/TCGA-18-3417-01Z-00-DX1.tif
      - ${INPUT_PATH_MASK}:/home/user/app/data/tcga/mask/TCGA-18-3417-01Z-00-DX1.tif
      - ${OUTPUT_PATH}:/home/user/app/data/outputs
    container_name: hlung
    deploy:
     resources:
       reservations:
         devices:
           - driver: nvidia
            #  count: 1
             device_ids: ["${GPU_DEVICE_IDS}"]
             capabilities: [gpu]
    entrypoint: ["python3", "-u", "-m", "heatmaps.heatmaps", "--wsi_name", "$WSI_NAME", "--sigma", "$SIGMA"]