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docker-compose-template.yml
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docker-compose-template.yml
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# This is a DivSeek Canada customized version of the docker-tripal
# sample configuration to run a Tripal instance with Docker-Compose
#
# This file is a template intended to be copied into an operational
# docker-compose.yml file, for crop-specific deployment customization.
# (NOTE: Please do NOT directly edit this file unless working on
# modifications or extensions that add CORE functionality to the Portal
# docker-compose build for all crop platforms being deployed.)
#
# (Meta)Data Persistence
# ======================
#
# NOTE: to allow the Tripal instance to store its (meta)data outside of its running containers,
# thus assuring persistence between container runs, this docker-compose.yml file configures
# a series of Docker 'named' "volumes". These are stored under the Docker installation directory.
#
# One can use the CLI command:
#
# docker exec -i -t <container_name> /bin/bash
#
# to directly log into each container to access data attached to each volume.
#
# Later iterations of this project may add additional services to facilitate access to, and backup of, these volumes.
#
# Application Port Visibility
# ===========================
#
# We've chosen to map the web sites - core and jbrowse - to TCP/IP ports 8082 and 8084, respectively.
# These ports are currently not publicly reserved for any other software product in the world.
#
version: '3'
services:
proxy:
image: nginx:latest
ports:
- "8200:80"
links:
- remoteuser
- apollo
- galaxy
- tripal
#- ngadmin
- chado_jb
- jbrowse
- jbrowse-graphql
- postgrest
#- postgrest_tripal
- postgraphql
- pgadmin4
volumes:
- "./nginx:/etc/nginx/conf.d"
remoteuser: ## Remote User Proxy for Apollo (based on Galaxy Auth)
image: "quay.io/erasche/gx-cookie-proxy:latest"
environment:
GALAXY_DB_URL: "postgresql://galaxy:galaxy@galaxy:5432/galaxy?client_encoding=utf8&sslmode=disable"
GALAXY_SECRET: "0xD1vS33kCanuck"
GXC_BACKEND_URL: "target:8080"
GXC_LOGLEVEL: DEBUG
links:
- galaxy
- apollo:target
galaxy: ## Galaxy, yay!
image: quay.io/galaxy-genome-annotation/docker-galaxy-annotation:master
environment:
NONUSE: nodejs,proftp,reports
PROXY_PREFIX: /galaxy
#
GALAXY_CHADO_DBHOST: "chado"
GALAXY_CHADO_DBNAME: "postgres"
GALAXY_CHADO_DBUSER: "postgres"
GALAXY_CHADO_DBPASS: "postgres"
GALAXY_CHADO_DBSCHEMA: "chado"
GALAXY_CHADO_DBPORT: 5432
#
GALAXY_LOGGING: full
GALAXY_CONFIG_COOKIE_PATH: /galaxy
GALAXY_CONFIG_BRAND: "GMOD"
#
GALAXY_WEBAPOLLO_URL: "http://apollo:8080/apollo"
GALAXY_WEBAPOLLO_EXT_URL: "/apollo"
GALAXY_WEBAPOLLO_PASSWORD: "password"
GALAXY_WEBAPOLLO_USER: [email protected]
#
GALAXY_SHARED_DIR: /apollo-data
GALAXY_JBROWSE_SHARED_DIR: /jbrowse/data
GALAXY_ID_SECRET: "0xD1vS33kCanuck"
volumes:
- "./volumes/apollo/apollo-data:/apollo-data" # shared with Apollo
- "./volumes/jbrowse/data:/jbrowse/data" # shared with JBrowse
- "./volumes/galaxy:/export"
- "./galaxy/galaxy.ini:/etc/galaxy/galaxy.ini"
apollo: ## Apollo, the genome annotation suite
image: quay.io/erasche/apollo:remote_user
links:
- "apollo_db"
- "chado"
environment:
CONTEXT_PATH: "apollo"
WEBAPOLLO_DB_USERNAME: postgres
WEBAPOLLO_DB_PASSWORD: postgres
WEBAPOLLO_DB_DRIVER: "org.postgresql.Driver"
WEBAPOLLO_DB_DIALECT: "org.hibernate.dialect.PostgresPlusDialect"
WEBAPOLLO_DB_URI: "jdbc:postgresql://apollo_db/postgres"
WEBAPOLLO_CHADO_DB_USERNAME: postgres
WEBAPOLLO_CHADO_DB_PASSWORD: postgres
WEBAPOLLO_CHADO_DB_DRIVER: "org.postgresql.Driver"
WEBAPOLLO_CHADO_DB_DIALECT: "org.hibernate.dialect.PostgresPlusDialect"
WEBAPOLLO_CHADO_DB_URI: "jdbc:postgresql://chado/postgres"
# Optional, allow image to 'wait'
WEBAPOLLO_DB_HOST: apollo_db
WEBAPOLLO_DB_PORT: 5432
WEBAPOLLO_DB_NAME: postgres
WEBAPOLLO_CHADO_DB_HOST: chado
WEBAPOLLO_CHADO_DB_PORT: 5432
WEBAPOLLO_CHADO_DB_NAME: postgres
#
APOLLO_PATH_PREFIX: "/apollo/"
#
# Configure admin user email
APOLLO_ADMIN_EMAIL: [email protected]
volumes:
- "./volumes/apollo/apollo-data:/apollo-data" # shared with Galaxy
apollo_db: ## Apollo's Postgres DB
image: postgres:9.5
environment:
POSTGRES_PASSWORD: postgres
volumes:
- "./volumes/apollo:/var/lib/postgresql/data/"
postgrest:
image: quay.io/erasche/postgrest:latest
links:
- "chado:db"
environment:
POSTGREST_JWT_SECRET: "D1vS33kCanuck"
POSTGREST_SCHEMA: chado
PG_PASSWORD: postgres
PG_DB: postgres
postgraphql: ## GraphQL interface to Postgres
image: erasche/postgraphql:gmod-hacks
environment:
DB_GRAPHQL_PATH: "/graphql"
DB_GRAPHIQL_PATH: "/graphiql"
PG_SECRET: "D1vS33kCanuck"
PGUSER: postgres
PGPASSWORD: postgres
PGHOST: chado
PGPORT: 5432
PGDATABASE: postgres
DB_SCHEMA: "public,chado"
links:
- chado
postgraphql-refseqs: ## PostGraphQL refseq server (required for JBrowse integration)
build: ./docker-gmod/refseqs
environment:
PGUSER: postgres
PGPASSWORD: postgres
PGHOST: chado
PGPORT: 5432
PGDATABASE: postgres
links:
- "chado:db"
pgadmin4: ## Postgres Admin Site
image: thajeztah/pgadmin4
ports:
- 8201:5050
links:
- "apollo_db:apollo"
- "chado:tripal"
volumes:
- "./pgadmin4.db:/pgadmin/config/pgadmin4.db"
chado_jb:
image: quay.io/erasche/chado-jbrowse-connector:latest
environment:
POSTGRES_PASSWORD: postgres
SITE_PATH: "${GMOD_BASE_URL_PROTO}${GMOD_SITE_BASE_HOSTNAME}/jbrowse/"
JBROWSE: "${GMOD_BASE_URL_PROTO}${GMOD_SITE_BASE_HOSTNAME}/jbrowse_actual/"
links:
- "chado:db"
tripal:
build:
context: ./tripal
dockerfile: Dockerfile
args:
DIVSEEK_ADMIN_USER: "${GMOD_ADMIN_USER}"
DIVSEEK_DB_HOST: "chado"
links:
- chado:postgres
volumes:
- ./volumes/tripal/html:/var/www/html/sites
- ./volumes/tripal/private:/var/www/private
environment:
UPLOAD_LIMIT: 20M
MEMORY_LIMIT: 128M
DB_HOST: "chado"
DB_NAME: "postgres"
#
SITE_NAME: "${GMOD_SITE_NAME}"
BASE_URL_PROTO: "${GMOD_BASE_URL_PROTO}"
BASE_URL_PATH: "${GMOD_BASE_URL_PATH}"
BASE_URL: "${GMOD_BASE_URL_PROTO}${GMOD_SITE_BASE_HOSTNAME}${GMOD_BASE_URL_PATH}"
#
TRIPAL_GIT_CLONE_LIBRARIES: "https://github.com/galaxyproject/blend4php.git"
TRIPAL_DOWNLOAD_MODULES: "bootstrap maillog smtp jquery_update panels advanced_help"
#
# BrAPI module fails to install correctly as of commit 962ffe4 of the tripal/brapi project
# TRIPAL_GIT_CLONE_MODULES: "https://github.com/tripal/tripal_jbrowse.git https://github.com/tripal/brapi"
# TRIPAL_ENABLE_MODULES: "bootstrap jquery_update panels advanced_help tripal_jbrowse page_manager tracker forum brapi"
#
TRIPAL_GIT_CLONE_MODULES: "https://github.com/tripal/tripal_jbrowse.git"
TRIPAL_ENABLE_MODULES: "bootstrap maillog smtp jquery_update panels advanced_help page_manager tracker forum tripal_jbrowse tripal_galaxy"
THEME: "bootstrap"
depends_on:
- chado
- elasticsearch
- jbrowse
chado: ## Tripal's Chado Database
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.
# The reason why is because Tripal will install the schema for us, but won't be able to run if there's an existing schema
INSTALL_CHADO_SCHEMA: 0
INSTALL_YEAST_DATA: 0
PGDATA: "/var/lib/postgresql/data/"
volumes:
- ./volumes/tripal/db:/var/lib/postgresql/data/
elasticsearch:
image: docker.elastic.co/elasticsearch/elasticsearch:6.5.1
environment:
TAKE_FILE_OWNERSHIP: "true"
volumes:
- ./volumes/index:/usr/share/elasticsearch/data
jbrowse:
image: quay.io/galaxy-genome-annotation/jbrowse:v1.12.5
volumes:
- "./volumes/jbrowse/data:/jbrowse/data" # shared with Galaxy
jbrowse-graphql:
image: quay.io/galaxy-genome-annotation/jbrowse:v1.12.5
volumes:
- "./docker-gmod/jbgraphql:/data"