diff --git a/stack_template.yml b/stack_template.yml deleted file mode 100755 index 68adc74b0148d4a44c653e1e0b1f12b538a6064b..0000000000000000000000000000000000000000 --- a/stack_template.yml +++ /dev/null @@ -1,286 +0,0 @@ -# ./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