compose-template.yml

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

version: '2'
services:
    proxy:
        image: quay.io/abretaud/nginx-ldap:latest # Not using the default nginx image as we need the ldap module
        ports:
            - "9170:80"
        links:
            - galaxy
            - jbrowse
            - tripal
            - apollo
            - apollo-report
            - blast
            - wiki
        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

    tripal:
        image: quay.io/galaxy-genome-annotation/tripal@sha256:4451cc3a601d109c07c7aedcc76bd41a5da7c438c8fa0862488680bd462f125b
        links:
            - tripaldb:postgres
            - elasticsearch:elasticsearch
        volumes_from:
            - "galaxy"
        volumes:
            - ./src_data:/data:ro
        environment:
            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"
            ENABLE_JBROWSE: /jbrowse/?data=data/gspecies
            ENABLE_APOLLO: 1
            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

    tripaldb:
        image: quay.io/galaxy-genome-annotation/chado:1.31-jenkins110.1-pg9.5
        environment:
            - POSTGRES_PASSWORD=postgres
            # The default chado image would try to install the schema on first run,
            # we just want the tools to be available.
            - INSTALL_CHADO_SCHEMA=0
        volumes:
            - ./docker_data/tripal_db/:/var/lib/postgresql/data/

    elasticsearch:
        image: docker.elastic.co/elasticsearch/elasticsearch:6.6.1
        #mem_limit: 500m   # This is to limit usage, but can make the docker crash when ram is exhausted, not recommended while indexing all data, ok once indexing is done
        ulimits:
            memlock:
                soft: -1
                hard: -1
        volumes:
            - ./docker_data/elastic_search_index/:/usr/share/elasticsearch/data
        environment: