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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,238 +1,3 @@ | ||
| version: '3' | ||
|
|
||
| services: | ||
| cbioportal: | ||
| restart: unless-stopped | ||
| image: ghcr.io/buschlab/cbioportal:${RELEASE:-latest} | ||
| container_name: cbioportal_container | ||
| environment: | ||
| HTTP_PROXY: "http://${HTTPS_PROXY_HOST}:${HTTPS_PROXY_PORT}" | ||
| NO_PROXY: "cbioportal" | ||
| volumes: | ||
| - ./study:/study/:z | ||
| - ./config/application.properties:/cbioportal/application.properties:Z | ||
| - ./config/security.properties:/cbioportal/security.properties:Z | ||
| - ./config/frontend.json:/cbioportal/frontend.json:Z | ||
| - ./config/${LOGO:-pm4onco.png}:/cbioportal-webapp/webapp/images/${LOGO:-pm4onco.png}:Z | ||
| - ./config/cacerts:/etc/ssl/certs/java/cacerts:Z | ||
| - cbioportal_portalinfo:/cbioportal/portalinfo:z | ||
| depends_on: | ||
| - cbioportal_database | ||
| - cbioportal-session | ||
| networks: | ||
| - cbioportal_net | ||
| command: [ | ||
| "/usr/bin/java", | ||
| "-Xms2g", | ||
| "-Xmx4g", | ||
| "-Doncokb.public_api.url=${ONCOKB_URL:-https://public.api.oncokb.org/api/v1}", | ||
| "-Doncokb.token=${ONCOKB_TOKEN}", | ||
| "-Dgenomenexus.url=/genome-nexus", | ||
| "-Dsession.service.url=http://cbioportal-session:5000/api/sessions/my-portal/", | ||
| "-Dshow.civic=${ENABLE_CIVIC:-true}", | ||
| "-Dmycancergenome.show=${ENABLE_MYCANCERGENOME:-false}", | ||
| "-Dquick_search.enabled=${ENABLE_QUICKSEARCH:-true}", | ||
| "-Dfilter_groups_by_appname=false", | ||
| "-Dhttps.proxyHost=${HTTPS_PROXY_HOST}", | ||
| "-Dhttps.proxyPort=${HTTPS_PROXY_PORT}", | ||
| "-Dhttp.nonProxyHosts=cbioportal-session|${NOPROXY_HOSTS:-}", | ||
| "-Dfrontend.config=/cbioportal/frontend.json", | ||
| "-Dskin.right_logo=${LOGO:-pm4onco.png}", | ||
| "-Dspring.config.location=cbioportal/application.properties", | ||
| "-Dauthenticate=${AUTHENTICATE:-false}", | ||
| "-Dspring.autoconfigure.exclude=${EXCLUDE_AUTOCONFIG:-org.springframework.boot.autoconfigure.security.SecurityAutoConfiguration}", | ||
| "-Dalways_show_study_group=${ALWAYS_SHOW_STUDY_GROUP:-none}", | ||
| "-Dspring.security.oauth2.client.provider.keycloak.user-name-attribute=email", | ||
| "-Dspring.security.oauth2.client.registration.keycloak.scope=openid,email,roles", | ||
| "-Dspring.security.oauth2.client.provider.keycloak.issuer-uri=${KEYCLOAK_REALM:-}", | ||
| "-Dspring.security.oauth2.client.registration.keycloak.client-id=${KEYCLOAK_CLIENT_CBIOPORTAL:-}", | ||
| "-Dspring.security.oauth2.client.registration.keycloak.client-secret=${KEYCLOAK_SECRET_CBIOPORTAL:-}", | ||
| "-Ddat.method=${DATA_ACCESS_TOKEN:-none}", | ||
| "-Ddat.oauth2.clientId=${KEYCLOAK_CLIENT_CBIOPORTAL:-}", | ||
| "-Ddat.oauth2.clientSecret=${KEYCLOAK_SECRET_CBIOPORTAL:-}", | ||
| "-Ddat.oauth2.issuer=${KEYCLOAK_REALM:-}", | ||
| "-Ddat.oauth2.accessTokenUri=${KEYCLOAK_REALM:-}/protocol/openid-connect/token", | ||
| "-Ddat.oauth2.userAuthorizationUri=${KEYCLOAK_REALM:-}/protocol/openid-connect/auth", | ||
| "-Ddat.oauth2.jwkUrl=${KEYCLOAK_REALM:-}/protocol/openid-connect/certs", | ||
| "-Ddat.oauth2.redirectUri=${CBIOPORTAL_URL}/api/data-access-token/oauth2", | ||
| "-Dsecurity.cors.allowed-origins=*", | ||
| "-Dserver.tomcat.remoteip.port-header=X-Forwarded-Port", | ||
| "-Dserver.tomcat.remoteip.protocol-header=X-Forwarded-Proto", | ||
| "-cp", | ||
| "/cbioportal-webapp:/cbioportal-webapp/lib/*", | ||
| "org.cbioportal.PortalApplication" | ||
| ] | ||
| cbioportal_database: | ||
| restart: unless-stopped | ||
| image: docker.io/mariadb:11.5.2 | ||
| container_name: cbioportal_database_container | ||
| environment: | ||
| MYSQL_ROOT_PASSWORD: ${MYSQL_ROOT_PASSWORD:-P@ssword1} | ||
| MYSQL_DATABASE: cbioportal | ||
| MYSQL_USER: cbio | ||
| MYSQL_PASSWORD: ${MYSQL_USER_PASSWORD:-P@ssword1} | ||
| security_opt: | ||
| - seccomp:unconfined | ||
| volumes: | ||
| - ./data/cgds.sql:/docker-entrypoint-initdb.d/cgds.sql:Z | ||
| - ./data/seed-cbioportal_hg19_hg38_v2.13.1.sql.gz:/docker-entrypoint-initdb.d/seed.sql.gz:Z | ||
| - ./data/tableExtension.sql:/docker-entrypoint-initdb.d/tableExtension.sql:Z | ||
| - cbioportal_data:/var/lib/mysql | ||
| command: | ||
| - --character-set-server=latin1 | ||
| - --collation-server=latin1_swedish_ci | ||
| - --innodb_buffer_pool_size=${INNODB_BUFFER_POOL_SIZE:-100M} | ||
| networks: | ||
| - cbioportal_net | ||
| cbioportal-session: | ||
| restart: unless-stopped | ||
| image: docker.io/cbioportal/session-service:0.6.1 | ||
| container_name: cbioportal_session_container | ||
| environment: | ||
| SERVER_PORT: 5000 | ||
| JAVA_OPTS: -Dspring.data.mongodb.uri=mongodb://cbioportal-session-database:27017/session-service | ||
| depends_on: | ||
| - cbioportal-session-database | ||
| networks: | ||
| - cbioportal_net | ||
| cbioportal-session-database: | ||
| restart: unless-stopped | ||
| image: docker.io/mongo:4.2 | ||
| container_name: cbioportal_session_database_container | ||
| environment: | ||
| MONGO_INITDB_DATABASE: session_service | ||
| volumes: | ||
| - cbioportal_session_data:/data/db | ||
| networks: | ||
| - cbioportal_net | ||
| fhirspark: | ||
| restart: unless-stopped | ||
| image: ghcr.io/buschlab/fhirspark:${RELEASE:-latest} | ||
| container_name: cbioportal_fhirspark | ||
| depends_on: | ||
| - hapiserver | ||
| environment: | ||
| FHIRSPARK_FHIRBASE: http://hapiserver:8080/fhir | ||
| FHIRSPARK_PORTALURL: http://cbioportal:8080/ | ||
| FHIRSPARK_LOGINREQUIRED: ${LOGINREQUIRED:-false} | ||
| volumes: | ||
| - ./data/drugs.json:/drugs.json:Z | ||
| - ./data/hgnc.csv:/hgnc.csv:Z | ||
| networks: | ||
| - cbioportal_net | ||
| hapiserver: | ||
| restart: unless-stopped | ||
| image: docker.io/hapiproject/hapi:v7.4.0-tomcat | ||
| container_name: cbioportal_fhirspark_hapiserver | ||
| depends_on: | ||
| - hapi-postgres | ||
| environment: | ||
| CATALINA_OPTS: | ||
| -Dhapi.fhir.server_address=${CBIOPORTAL_URL}/fhir | ||
| -Dhapi.fhir.local_base_url=http://hapiserver:8080/fhir | ||
| -Dhapi.fhir.reuse_cached_search_results_millis=5000 | ||
| -Dhapi.fhir.validation.requests_enabled=false | ||
| -Dspring.datasource.url=jdbc:postgresql://hapi-postgres:5432/hapi?currentSchema=public | ||
| -Dspring.datasource.username=hapiserver | ||
| -Dspring.datasource.password=${POSTGRES_USER_PASSWORD:-P@ssword2} | ||
| -Dspring.datasource.driverClassName=org.postgresql.Driver | ||
| -Dspring.jpa.properties.hibernate.dialect=ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect | ||
| networks: | ||
| - cbioportal_net | ||
| hapi-postgres: | ||
| restart: unless-stopped | ||
| image: docker.io/postgres:16.4-alpine | ||
| container_name: cbioportal_fhirspark_database | ||
| volumes: | ||
| - fhir_data:/var/lib/postgresql/data | ||
| environment: | ||
| POSTGRES_USER: hapiserver | ||
| POSTGRES_PASSWORD: ${POSTGRES_USER_PASSWORD:-P@ssword2} | ||
| POSTGRES_DB: hapi | ||
| networks: | ||
| - cbioportal_net | ||
| cbioproxy: | ||
| restart: unless-stopped | ||
| image: ghcr.io/buschlab/cbioproxy:${RELEASE:-latest} | ||
| container_name: cbioproxy_container | ||
| volumes: | ||
| - ./services/cbioproxy/nginx.conf:/usr/local/openresty/nginx/conf/nginx.conf:Z | ||
| - ./services/cbioproxy/cbioportal.conf:/cbioportal.conf:Z | ||
| - ./services/cbioproxy/lua_auth_config.lua:/etc/nginx/conf.d/lua_auth_config.lua:Z | ||
| - ./services/cbioproxy/lua_login_config.lua:/etc/nginx/conf.d/lua_login_config.lua:Z | ||
| - ./services/cbioproxy/lua_resource_config.lua:/etc/nginx/conf.d/lua_resource_config.lua:Z | ||
| - ./reports:/usr/share/reports:Z | ||
| - ./config/attributes.json:/attributes.json:Z | ||
| - ./data/tumorTypes.json:/tumorTypes.json:Z | ||
| - ./config/keycloak.pem:/keycloak.pem:z | ||
| environment: | ||
| NGINX_LOGINREQUIRED: ${LOGINREQUIRED:-false} | ||
| KEYCLOAK_REALM: ${KEYCLOAK_REALM:-} | ||
| KEYCLOAK_CLIENT_FHIRSPARK: ${KEYCLOAK_CLIENT_FHIRSPARK:-fhirspark} | ||
| KEYCLOAK_SECRET_FHIRSPARK: ${KEYCLOAK_SECRET_FHIRSPARK:-nosecrethere} | ||
| CBIOPORTAL_URL: ${CBIOPORTAL_URL:-//localhost:8080} | ||
| PORT: ${PORT:-8080} | ||
| ports: | ||
| - "${PORT:-8080}:8080" | ||
| depends_on: | ||
| - cbioportal | ||
| - fhirspark | ||
| - genomenexus | ||
| networks: | ||
| - cbioportal_net | ||
| genomenexus: | ||
| image: ghcr.io/buschlab/genome-nexus:${RELEASE:-latest} | ||
| environment: | ||
| - SERVER_PORT=8888 | ||
| restart: unless-stopped | ||
| depends_on: | ||
| - genomenexus_db | ||
| - ensembl-rest | ||
| - ensembl-mysql | ||
| command: [ | ||
| "-Dhttps.proxyHost=${HTTPS_PROXY_HOST}", | ||
| "-Dhttps.proxyPort=${HTTPS_PROXY_PORT}", | ||
| "-Dspring.data.mongodb.uri=mongodb://genomenexus_db:27017/annotator", | ||
| "-Dvep.url=http://ensembl-rest:3000/vep/human/hgvs/VARIANT?content-type=application/json&xref_refseq=1&ccds=1&canonical=1&domains=1&hgvs=1&numbers=1&protein=1", | ||
| "-Dgenexrefs.url=http://ensembl-rest:3000/xrefs/id/ACCESSION?content-type=application/json", | ||
| "-Densembl.sequence.url=http://localhost:3000/sequence/region/human/QUERY?content-type=application/json", | ||
| "-DmutationAssessor.url=http://127.0.0.1/VARIANT&frm=json&fts=input,rgaa,rgvt,msa,pdb,F_impact,F_score,vc_score,vs_score,info,var,gene,uprot,rsprot,gaps,msa_height,chr,rs_pos,rs_res,up_pos,up_res,cnt_cosmic,cnt_snps", | ||
| "-jar", | ||
| "/app/genome-nexus.war" | ||
| ] | ||
| networks: | ||
| - cbioportal_net | ||
| genomenexus_db: | ||
| image: docker.io/genomenexus/gn-mongo:0.31 | ||
| volumes: | ||
| - genomenexus_data:/bitnami/mongodb | ||
| environment: | ||
| - REF_ENSEMBL_VERSION=grch37_ensembl92 | ||
| - SPECIES=homo_sapiens | ||
| restart: unless-stopped | ||
| networks: | ||
| - cbioportal_net | ||
| ensembl-rest: | ||
| image: docker.io/nr205/ensembl-rest:111 | ||
| restart: unless-stopped | ||
| volumes: | ||
| - ./config/ensembl_rest.conf:/opt/vep/src/ensembl-rest/ensembl_rest.conf:Z | ||
| networks: | ||
| - cbioportal_net | ||
| depends_on: | ||
| - ensembl-mysql | ||
| ensembl-mysql: | ||
| image: ghcr.io/buschlab/ensembl-mysql:latest | ||
| restart: unless-stopped | ||
| networks: | ||
| - cbioportal_net | ||
|
|
||
| networks: | ||
| cbioportal_net: | ||
|
|
||
| volumes: | ||
| cbioportal_data: | ||
| cbioportal_session_data: | ||
| cbioportal_portalinfo: | ||
| fhir_data: | ||
| genomenexus_data: | ||
| include: | ||
| - ./compose/base.yml | ||
| - ./compose/${FLAVOR:-care}.yml |
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