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# ./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