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compose-research.yml
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compose-research.yml
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version: '3'
services:
cbioportal:
restart: unless-stopped
image: docker.io/cbioportal/cbioportal:6.0.4
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/${LOGO:-pm4onco.png}:/cbioportal-webapp/webapp/images/${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: [
"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:-true}",
"-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:-}",
"-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
cbioproxy:
restart: unless-stopped
image: ghcr.io/buschlab/cbioproxy:${RELEASE:-latest}
environment:
NGINX_LOGINREQUIRED: ${LOGINREQUIRED:-false}
PORT: ${PORT:-8080}
container_name: cbioproxy_container
volumes:
- ./services/cbioproxy/nginx.conf:/usr/local/openresty/nginx/conf/nginx.conf:Z
- ./services/cbioproxy/cbioportal-research.conf:/cbioportal.conf:Z
- ./services/cbioproxy/lua_resource_config.lua:/etc/nginx/conf.d/lua_resource_config.lua:Z
- ./reports:/usr/share/reports:Z
ports:
- "${PORT:-8080}:8080"
depends_on:
- cbioportal
- 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:
genomenexus_data: