Delete stack_template.yml

stack_template.yml

-# ./docker_data is created and filled with persistent data that should be backuped
-
-version: '3.7'
-services:
-    proxy:
-        image: quay.io/abretaud/nginx-ldap:latest
-        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
-        networks:
-            - traefik
-            - genus_species
-        deploy:
-          labels:
-            # Download page
-            - "traefik.http.routers.genus_species-nginx.rule=(Host(`localhost`) && PathPrefix(`/sp/genus_species/download`))"
-            - "traefik.http.routers.genus_species-nginx.tls=true"
-            - "traefik.http.routers.genus_species-nginx.entryPoints=webs"
-            - "traefik.http.routers.genus_species-nginx.middlewares=sp-auth,sp-app-trailslash,sp-prefix"
-            - "traefik.http.services.genus_species-nginx.loadbalancer.server.port=80"
-          restart_policy:
-            condition: on-failure
-            delay: 5s
-            max_attempts: 3
-            window: 120s
-
-    tripal:
-        image: quay.io/galaxy-genome-annotation/tripal:v2.x
-        depends_on:
-            - tripal-db
-            - elasticsearch
-        volumes:
-            - ./docker_data/galaxy/:/export/:ro
-            - ./src_data/:/project_data/:ro
-            - ./src_data:/data:ro
-            #- /groups/XXX/:/groups/XXX/:ro  # We do this when we have symlinks in src_data pointing to /groups/XXX/...
-        environment:
-            DB_HOST: tripal-db.genus_species
-            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"
-            ELASTICSEARCH_HOST: elasticsearch.genus_species
-            ENABLE_JBROWSE: /jbrowse/?data=data/gspecies
-            ENABLE_APOLLO: https://localhost/apollo/
-            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
-        networks:
-            - traefik
-            - genus_species
-        deploy:
-          labels:
-            - "traefik.http.routers.genus_species-tripal.rule=(Host(`localhost`) && PathPrefix(`/sp/genus_species`))"
-            - "traefik.http.routers.genus_species-tripal.tls=true"
-            - "traefik.http.routers.genus_species-tripal.entryPoints=webs"
-            - "traefik.http.routers.genus_species-tripal.middlewares=sp-auth,sp-trailslash,sp-prefix,tripal-addprefix"
-            - "traefik.http.services.genus_species-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-jenkins26-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/
-        networks:
-            - genus_species
-
-    elasticsearch:
-        image: docker.elastic.co/elasticsearch/elasticsearch:6.6.1
-        #deploy:
-          #resources:
-            #limits:
-              #memory: 500M
-        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: "-Xms500m -Xmx500m"
-            TAKE_FILE_OWNERSHIP: "true"
-        networks:
-            - genus_species
-
-    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/
-            - ../galaxy_nginx.conf:/etc/nginx/uwsgi_params
-        environment:
-            NONUSE: nodejs,proftp,reports,condor
-            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_TRIPAL_URL: http://tripal.genus_species/tripal/
-            GALAXY_TRIPAL_PASSWORD: XXXXXX  # See tripal config above
-            GALAXY_WEBAPOLLO_URL: http://one-of-the-swarm-node:8888/apollo/
-            GALAXY_WEBAPOLLO_USER: "admin_apollo@bipaa"
-            GALAXY_WEBAPOLLO_PASSWORD: "XXXXXX"  # See tripal config below
-            GALAXY_WEBAPOLLO_EXT_URL: /apollo/
-            GALAXY_CHADO_DBHOST: tripal-db.genus_species
-            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
-            master_api_key: MASTERLOCK
-        networks:
-            - traefik
-            - genus_species
-        deploy:
-          labels:
-            - "traefik.http.routers.genus_species-galaxy.rule=(Host(`localhost`) && PathPrefix(`/sp/genus_species/galaxy`))"
-            - "traefik.http.routers.genus_species-galaxy.tls=true"
-            - "traefik.http.routers.genus_species-galaxy.entryPoints=webs"
-            - "traefik.http.routers.genus_species-galaxy.middlewares=sp-auth,sp-app-trailslash,sp-app-prefix"
-            - "traefik.http.services.genus_species-galaxy.loadbalancer.server.port=80"
-          restart_policy:
-            condition: on-failure
-            delay: 5s
-            max_attempts: 3
-            window: 120s
-
-    jbrowse:
-        image: quay.io/galaxy-genome-annotation/jbrowse:v1.16.8
-        volumes:
-            - ./docker_data/galaxy/:/export/:ro
-            - ./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/:ro
-        networks:
-            - traefik
-            - genus_species
-        deploy:
-          labels:
-            - "traefik.http.routers.genus_species-jbrowse.rule=(Host(`localhost`) && PathPrefix(`/sp/genus_species/jbrowse`))"
-            - "traefik.http.routers.genus_species-jbrowse.tls=true"
-            - "traefik.http.routers.genus_species-jbrowse.entryPoints=webs"
-            - "traefik.http.routers.genus_species-jbrowse.middlewares=sp-auth,sp-app-trailslash,sp-app-prefix"
-            - "traefik.http.services.genus_species-jbrowse.loadbalancer.server.port=80"
-          restart_policy:
-            condition: on-failure
-            delay: 5s
-            max_attempts: 3
-            window: 120s
-
-    blast:
-        image: quay.io/abretaud/sf-blast:latest
-        depends_on:
-            - blast-db
-        environment:
-            DB_HOST: blast-db.genus_species
-            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-3.7.1.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)
-            #JOBS_DRMAA_NATIVE: '-p web' # This line and following for slurm
-            #DRMAA_METHOD: 'slurm' # This line and following for slurm
-        volumes:
-            #- ../blast-themes/xxx/:/var/www/blast/app/Resources/:ro # You can theme the app
-            #- /data1/sge/:/usr/local/sge/:ro # an 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
-            #- /data1/slurm/slurm.conf:/etc/slurm-llnl/slurm.conf:ro # This line and following for slurm
-            #- /data1/slurm/gres.conf:/etc/slurm-llnl/gres.conf:ro
-            #- /data1/slurm/cgroup.conf:/etc/slurm-llnl/cgroup.conf:ro
-            #- /data1/slurm/slurmdbd.conf:/etc/slurm-llnl/slurmdbd.conf:ro
-            #- /data1/slurm/drmaa/:/etc/slurm-llnl/drmaa/:ro
-            #- /etc/munge/:/etc/munge/:ro
-        networks:
-            - traefik
-            - genus_species
-        deploy:
-          labels:
-            - "traefik.http.routers.genus_species-blast.rule=(Host(`localhost`) && PathPrefix(`/sp/genus_species/blast`))"
-            - "traefik.http.routers.genus_species-blast.tls=true"
-            - "traefik.http.routers.genus_species-blast.entryPoints=webs"
-            - "traefik.http.routers.genus_species-blast.middlewares=sp-big-req,sp-auth,sp-app-trailslash,sp-app-prefix"
-            - "traefik.http.services.genus_species-blast.loadbalancer.server.port=80"
-          restart_policy:
-            condition: on-failure
-            delay: 5s
-            max_attempts: 3
-            window: 120s
-
-    blast-db:
-        image: postgres:9.6-alpine
-        environment:
-            - POSTGRES_PASSWORD=postgres
-            - PGDATA=/var/lib/postgresql/data/
-        volumes:
-            - ./docker_data/blast_db/:/var/lib/postgresql/data/
-        networks:
-            - genus_species
-
-    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_HOST: wiki-db.genus_species
-            MEDIAWIKI_DB_PASSWORD: password
-            MEDIAWIKI_ADMIN_USER: abretaud   # ldap user
-        depends_on:
-            - wiki-db
-        volumes:
-            - ./docker_data/wiki_uploads:/images
-            #- ../bipaa_wiki.png:/var/www/mediawiki/resources/assets/wiki.png:ro # To change the logo at the top left
-        networks:
-            - traefik
-            - genus_species
-        deploy:
-          labels:
-            - "traefik.http.routers.genus_species-blast.rule=(Host(`localhost`) && PathPrefix(`/sp/genus_species/blast`))"
-            - "traefik.http.routers.genus_species-blast.tls=true"
-            - "traefik.http.routers.genus_species-blast.entryPoints=webs"
-            - "traefik.http.routers.genus_species-blast.middlewares=sp-big-req,sp-auth,sp-app-trailslash,sp-app-prefix"
-            - "traefik.http.services.genus_species-blast.loadbalancer.server.port=80"
-          restart_policy:
-            condition: on-failure
-            delay: 5s
-            max_attempts: 3
-            window: 120s
-
-    wiki-db:
-        image: postgres:9.6-alpine
-        volumes:
-            - ./docker_data/wiki_db/:/var/lib/postgresql/data/
-        networks:
-            - genus_species
-
-networks:
-    traefik:
-        external: true
-    genus_species:
-        driver: overlay
-        name: genus_species