docker-compose.yml

# ./docker_data is created and filled with persistent data that should be backuped

version: '3.7'
services:
    proxy:
        image: quay.io/abretaud/nginx-ldap:latest
        volumes:
            - ./src_data/:/project_data/
            #- /groups/XXX/:/groups/XXX/:ro  # We do this when we have symlinks in src_data pointing to /groups/XXX/...
            - ./nginx/conf:/etc/nginx/conf.d
        networks:
            - traefik
            - genus_species
        deploy:
          labels:
            # Download page
            - "traefik.http.routers.genus_species-nginx.rule=(Host(`localhost`) && PathPrefix(`/sp/genus_species/download`))"
            - "traefik.http.routers.genus_species-nginx.tls=true"
            - "traefik.http.routers.genus_species-nginx.entryPoints=webs"
            - "traefik.http.routers.genus_species-nginx.middlewares=sp-auth,sp-app-trailslash,sp-prefix"
            - "traefik.http.services.genus_species-nginx.loadbalancer.server.port=80"
          restart_policy:
            condition: on-failure
            delay: 5s
            max_attempts: 3
            window: 120s

    tripal:
        image: quay.io/galaxy-genome-annotation/tripal:v2.x
        depends_on:
            - tripal-db
            - elasticsearch
        volumes:
            - ./docker_data/galaxy/:/export/:ro
            - ./src_data/:/project_data/:ro
            - ./src_data:/data:ro
            #- /groups/XXX/:/groups/XXX/:ro  # We do this when we have symlinks in src_data pointing to /groups/XXX/...
        environment:
            DB_HOST: tripal-db.genus_species
            BASE_URL_PATH: /sp/genus_species
            UPLOAD_LIMIT: 20M
            MEMORY_LIMIT: 512M
            TRIPAL_GIT_CLONE_MODULES: "https://github.com/abretaud/tripal_rest_api.git[@c6f9021ea5d4c6d7c67c5bd363a7dd9359228bbc] https://github.com/tripal/tripal_elasticsearch.git[@dc7f276046e394a80a7dfc9404cf1a149006eb2a] https://github.com/tripal/tripal_analysis_interpro.git https://github.com/tripal/tripal_analysis_go.git https://github.com/tripal/tripal_analysis_blast.git  https://github.com/tripal/tripal_analysis_expression.git[@7240039fdeb4579afd06bbcb989cb7795bd4c342]"
            TRIPAL_DOWNLOAD_MODULES: ""
            TRIPAL_ENABLE_MODULES: "tripal_analysis_blast tripal_analysis_interpro tripal_analysis_go tripal_rest_api tripal_elasticsearch"
            SITE_NAME: "Genus species"
            ELASTICSEARCH_HOST: elasticsearch.genus_species
            ENABLE_JBROWSE: /jbrowse/?data=data/gspecies
            ENABLE_APOLLO: https://localhost/apollo/
            ENABLE_BLAST: 1
            ENABLE_DOWNLOAD: 1
            ENABLE_WIKI: 1
            ENABLE_GO: /organism/Genus/species?pane=GO
            ENABLE_ORTHOLOGY: 0
            ENABLE_ORTHOLOGY_LINKS: http://localhost/sp/orthology/
            #THEME: "bipaa"    # Use this to use another theme
            #THEME_GIT_CLONE: "https://gitlab.inria.fr/abretaud/tripal_bipaa.git"    # Use this to install another theme
            ADMIN_PASSWORD: XXXXXX  # You need to define it and update it in galaxy config below
        networks:
            - traefik
            - genus_species
        deploy:
          labels:
            - "traefik.http.routers.genus_species-tripal.rule=(Host(`localhost`) && PathPrefix(`/sp/genus_species`))"
            - "traefik.http.routers.genus_species-tripal.tls=true"
            - "traefik.http.routers.genus_species-tripal.entryPoints=webs"
            - "traefik.http.routers.genus_species-tripal.middlewares=sp-auth,sp-trailslash,sp-prefix,tripal-addprefix"
            - "traefik.http.services.genus_species-tripal.loadbalancer.server.port=80"
          restart_policy:
            condition: on-failure