From 65f38814a056655e3136df61abfb4630fa4fd5f0 Mon Sep 17 00:00:00 2001 From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr> Date: Thu, 9 Apr 2020 16:41:03 +0200 Subject: [PATCH] Delete compose-template.yml --- compose-template.yml | 229 ------------------------------------------- 1 file changed, 229 deletions(-) delete mode 100755 compose-template.yml diff --git a/compose-template.yml b/compose-template.yml deleted file mode 100755 index ee3e04e..0000000 --- a/compose-template.yml +++ /dev/null @@ -1,229 +0,0 @@ -# ./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/ -- GitLab