# ./docker_data is created and filled with persistent data that should be backuped version: '3.7' services: tripal: image: quay.io/galaxy-genome-annotation/tripal:v2.x depends_on: - tripal-db volumes: - ./docker_data/galaxy/:/export/:ro - ./src_data/:/data/:ro environment: DB_HOST: tripal-db.orthology BASE_URL_PATH: /sp/orthology UPLOAD_LIMIT: 20M MEMORY_LIMIT: 512M TRIPAL_GIT_CLONE_MODULES: "https://github.com/abretaud/tripal_rest_api.git[@c6f9021ea5d4c6d7c67c5bd363a7dd9359228bbc] https://github.com/abretaud/tripal_linkout.git[@91e08a11b788f005631cc0fafa4d68b1d2ce3ceb] https://github.com/abretaud/tripal_phylotree.git[@4cad769c9deaa5cd2933e1ae29be6aea8c8c0cc2]" TRIPAL_DOWNLOAD_MODULES: "" TRIPAL_ENABLE_MODULES: "tripal_rest_api tripal_phylotree tripal_linkout" SITE_NAME: "Orthology" ENABLE_JBROWSE: 0 ENABLE_APOLLO: 0 ENABLE_BLAST: 0 ENABLE_DOWNLOAD: 0 ENABLE_WIKI: 0 ENABLE_GO: 0 ENABLE_ORTHOLOGY: 1 # Must match the SITE_NAME in the gcv part GCV_SITE_NAME: "example" # Use this to point to the external adress of your main tripal host MAIN_TRIPAL_URL: "http://{{ hostname }}" #THEME: "{{ tripal_theme_name }}" # Use this to use another theme #THEME_GIT_CLONE: "{{ tripal_theme_git_clone }}" # Use this to install another theme ADMIN_PASSWORD: {{ tripal_password }} # You need to define it and update it in galaxy config below networks: - traefikbig - orthology deploy: labels: - "traefik.http.routers.orthology-tripal.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/orthology`))" - "traefik.http.routers.orthology-tripal.tls=true" - "traefik.http.routers.orthology-tripal.entryPoints=webs" - "traefik.http.routers.orthology-tripal.middlewares=sp-auth,sp-trailslash,sp-prefix,tripal-addprefix" - "traefik.http.services.orthology-tripal.loadbalancer.server.port=80" restart_policy: condition: on-failure delay: 5s max_attempts: 3 window: 120s tripal-db: image: quay.io/galaxy-genome-annotation/chado:1.31-jenkins21-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 - INSTALL_YEAST_DATA=0 volumes: - ./docker_data/tripal_db/:/var/lib/postgresql/data/ networks: - orthology gcv: image: quay.io/abretaud/lis-gcv depends_on: - tripal-db environment: DB_HOST: tripal-db.orthology HOST: {{ hostname }} SITE_NAME: example SITE_FULL_NAME: example DEBUG: "false" GCV_URL: http://{{ hostname }}/sp/orthology/gcv SERVICES_URL: http://{{ hostname }}/sp/orthology/gcv_api/services TRIPAL_URL: http://{{ hostname }}/sp/orthology/ USE_GENE_UNAME: "true" networks: - traefikbig - orthology deploy: labels: - "traefik.http.routers.orthology-gcv.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/orthology/gcv`))" - "traefik.http.routers.orthology-gcv.tls=true" - "traefik.http.routers.orthology-gcv.entryPoints=webs" - "traefik.http.routers.orthology-gcv.service=orthology-gcv" - "traefik.http.routers.orthology-gcv.middlewares=sp-auth,sp-app-trailslash,sp-app-prefix" - "traefik.http.services.orthology-gcv.loadbalancer.server.port=80" - "traefik.http.routers.orthology-gcv-api.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/orthology/gcv_api`))" - "traefik.http.routers.orthology-gcv-api.tls=true" - "traefik.http.routers.orthology-gcv-api.entryPoints=webs" - "traefik.http.routers.orthology-gcv-api.service=orthology-gcv-api" - "traefik.http.routers.orthology-gcv-api.middlewares=sp-auth,sp-app-trailslash,sp-app-prefix" - "traefik.http.services.orthology-gcv-api.loadbalancer.server.port=8000" restart_policy: condition: on-failure delay: 5s max_attempts: 3 window: 120s galaxy: image: quay.io/galaxy-genome-annotation/docker-galaxy-annotation:gmod volumes: - ../galaxy_data_libs_SI.py:/opt/setup_data_libraries.py - ./docker_data/galaxy/:/export/ - ./src_data/:/project_data/:ro #- /groups/XXX/:/groups/XXX/:ro # We do this when we have symlinks in src_data pointing to /groups/XXX/... environment: NONUSE: nodejs,proftp,reports,condor GALAXY_LOGGING: full GALAXY_CONFIG_BRAND: "Orthology" GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE: "True" GALAXY_CONFIG_USE_REMOTE_USER: "True" GALAXY_CONFIG_REMOTE_USER_MAILDOMAIN: "bipaa" GALAXY_CONFIG_ADMIN_USERS: "admin@galaxy.org,gogepp@bipaa" # admin@galaxy.org is the default (leave it), gogepp@bipaa is a shared ldap user we use to connect ENABLE_FIX_PERMS: 0 PROXY_PREFIX: /sp/orthology/galaxy GALAXY_TRIPAL_URL: http://tripal.orthology/tripal/ GALAXY_TRIPAL_PASSWORD: {{ tripal_password }} # See tripal config above GALAXY_CHADO_DBHOST: tripal-db.orthology GALAXY_CHADO_DBSCHEMA: chado GALAXY_AUTO_UPDATE_DB: 1 GALAXY_AUTO_UPDATE_CONDA: 1 GALAXY_AUTO_UPDATE_TOOLS: "/galaxy-central/tools_1.yaml" GALAXY_SHARED_DIR: "" BLAT_ENABLED: 1 networks: - traefikbig - orthology deploy: labels: - "traefik.http.routers.orthology-galaxy.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/orthology/galaxy`))" - "traefik.http.routers.orthology-galaxy.tls=true" - "traefik.http.routers.orthology-galaxy.entryPoints=webs" - "traefik.http.routers.orthology-galaxy.middlewares=sp-auth,sp-app-trailslash,sp-app-prefix" - "traefik.http.services.orthology-galaxy.loadbalancer.server.port=80" restart_policy: condition: on-failure delay: 5s max_attempts: 3 window: 120s networks: traefikbig: external: true orthology: driver: overlay name: orthology