# ./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:
bootstrap.memory_lock: "true"
xpack.security.enabled: "false"
xpack.monitoring.enabled: "false"
xpack.ml.enabled: "false"
xpack.graph.enabled: "false"
xpack.watcher.enabled: "false"
cluster.routing.allocation.disk.threshold_enabled: "false"
ES_JAVA_OPTS: "-Xms200m -Xmx200m"
TAKE_FILE_OWNERSHIP: "true"
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/...
- ./docker_data/jbrowse/:/jbrowse/data/
- ./docker_data/apollo/:/apollo-data/
links:
- "tripaldb:chado"
environment:
NONUSE: nodejs,proftp,reports
GALAXY_LOGGING: full
GALAXY_CONFIG_BRAND: "Genus species"
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/genus_species/galaxy
GALAXY_CONFIG_COOKIE_PATH: /galaxy
GALAXY_TRIPAL_PASSWORD: XXXXXX # See tripal config above
GALAXY_WEBAPOLLO_URL: http://apollo:8080
GALAXY_WEBAPOLLO_USER: "admin_apollo@bipaa"
GALAXY_WEBAPOLLO_PASSWORD: "XXXXXX" # See tripal config below
GALAXY_WEBAPOLLO_EXT_URL: /sp/genus_species/apollo
GALAXY_CHADO_DBHOST: chado
GALAXY_CHADO_DBSCHEMA: chado
GALAXY_AUTO_UPDATE_DB: 1
GALAXY_AUTO_UPDATE_CONDA: 1
GALAXY_AUTO_UPDATE_TOOLS: "/galaxy-central/tools_1.yaml"
BLAT_ENABLED: 1
jbrowse:
image: quay.io/galaxy-genome-annotation/jbrowse:v1.16.5
volumes:
- /data
volumes_from:
- "galaxy:ro"
ports:
- "80"
apollo:
image: quay.io/abretaud/apollo:bipaa
links:
- "apollo_db:db"
environment:
APOLLO_ADMIN_EMAIL: "admin_apollo@bipaa" # internal admin user, used by some scripts/api
APOLLO_ADMIN_PASSWORD: "XXXXXX" # define it and adapt galaxy config above
APOLLO_BASE_HOST: "http://localhost"
APOLLO_PATH_PREFIX: "/sp/genus_species/apollo/"
APOLLO_REMOTE_ADMINS: "gogepp@bipaa,abretaud@bipaa,srobin@bipaa,flegeai@bipaa" # all ldap users that we use to connect as admin
WEBAPOLLO_DB_USERNAME: postgres
WEBAPOLLO_DB_PASSWORD: password
WEBAPOLLO_DB_DRIVER: "org.postgresql.Driver"
WEBAPOLLO_DB_DIALECT: "org.hibernate.dialect.PostgresPlusDialect"
WEBAPOLLO_DB_URI: "jdbc:postgresql://db/postgres"
WEBAPOLLO_FEATURE_HAS_DBXREFS: "true"
WEBAPOLLO_FEATURE_HAS_ATTRS: "true"
WEBAPOLLO_FEATURE_HAS_PUBMED: "true"
WEBAPOLLO_FEATURE_HAS_GO: "true"
WEBAPOLLO_FEATURE_HAS_COMMENTS: "true"
WEBAPOLLO_FEATURE_HAS_STATUS: "true"
CATALINA_OPTS: "-Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC"
volumes_from:
- "galaxy:ro"
volumes:
- ./apollo/annotation_groups.tsv:/bootstrap/canned_values.txt:ro # Other canned things are preloaded in the docker image https://github.com/abretaud/docker-apollo/blob/bipaa/bootstrap.sh
#- ../blat/:/opt/blat/:ro # Mount the blat binary if you want to use it (could not include it in the docker image due to license issue)
apollo_db:
image: postgres:9.5
environment:
POSTGRES_PASSWORD: password
volumes:
- ./docker_data/apollo_db/:/var/lib/postgresql/data/
apollo-report: # A report app following guidelines from https://bipaa.genouest.org/is/how-to-annotate-a-genome/
links:
- apollo:apollo
image: quay.io/abretaud/apollo-report:latest
environment:
APOLLO_EXT_URL: http://localhost/sp/genus_species/apollo/
APOLLO_USER: admin_apollo@bipaa
APOLLO_PASS: XXXXX # See apollo conf above
ADMIN_USERS: login1,login2 # ldap users that should see an extended report
APOLLO_MOUNTPOINT: /apollo-data/
volumes:
- ./docker_data/apollo/:/apollo-data/:ro
- ./apollo/annotation_groups.tsv:/data/annotation_groups.tsv:ro
- ./docker_data/apollo_report/:/data/report/
blast:
image: quay.io/abretaud/sf-blast:latest
links:
- blast_db:postgres
#hostname: gogepp-blast.genouest.org # Hostname declare as submit node in sge conf (for drmaa mode only)
environment:
UPLOAD_LIMIT: 20M
MEMORY_LIMIT: 128M
DB_NAME: 'postgres'
ADMIN_EMAIL: 'xxx@example.org' # email sender
ADMIN_NAME: 'xxxxx' # email sender name
JOBS_METHOD: 'local' # Can be local (= no sge jobs, but run inside the container) or drmaa (= to submit to a cluster)
JOBS_WORK_DIR: '/xxxx/blast_jobs/' # disk accessible both from compute nodes and mounted in this docker (at the same path)
CDD_DELTA_PATH: '/db/cdd_delta/current/flat/cdd_delta'
BLAST_TITLE: 'Genus species blast server'
JOBS_SCHED_NAME: 'blast_gspecies' # job names
PRE_CMD: '. /local/env/envblast-2.6.0.sh; . /local/env/envpython-2.7.sh;' # executed at the beginning of each job
APACHE_RUN_USER: 'bipaaweb' # username known by sge
APACHE_RUN_GROUP: 'bipaa' # group known by sge
BASE_URL_PATH: '/sp/genus_species/blast/'
UID: 55914 # username known by sge (for drmaa mode only)
GID: 40259 # group known by sge (for drmaa mode only)
volumes:
#- ../blast-themes/xxx/:/var/www/blast/app/Resources/:ro # You can theme the app
- /data1/sge/:/usr/local/sge/:ro # the sge install
#- /xxxx/blast_jobs/:/xxxx/blast_jobs/ # (for drmaa mode only)
- ./blast/banks.yml:/var/www/blast/app/config/banks.yml:ro
- ./blast/links.yml:/etc/blast_links/links.yml:ro
blast_db:
image: postgres:9.5
environment:
- POSTGRES_PASSWORD=postgres
- PGDATA=/var/lib/postgresql/data/
volumes:
- ./docker_data/blast_db/:/var/lib/postgresql/data/
wiki:
image: quay.io/abretaud/mediawiki
environment:
MEDIAWIKI_SERVER: http://localhost
MEDIAWIKI_PROXY_PREFIX: /sp/genus_species/wiki
MEDIAWIKI_SITENAME: Genus species
MEDIAWIKI_SECRET_KEY: XXXXXXXXXX
MEDIAWIKI_DB_PASSWORD: password
MEDIAWIKI_ADMIN_USER: abretaud # ldap user
links:
- wiki_db:db
volumes:
- ./docker_data/wiki_uploads:/images
#- ../bipaa_wiki.png:/var/www/mediawiki/resources/assets/wiki.png:ro # To cange the logo at the top left
wiki_db:
image: postgres:9.5
volumes:
- ./docker_data/wiki_db/:/var/lib/postgresql/data/