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apiVersion: extensions/v1beta1
kind: Deployment
metadata:
annotations:
deployment.kubernetes.io/revision: "4"
creationTimestamp: null
generation: 1
labels:
run: cbioportal-spring-boot
name: cbioportal-spring-boot
selfLink: /apis/extensions/v1beta1/namespaces/default/deployments/cbioportal-spring-boot
spec:
replicas: 2
selector:
matchLabels:
run: cbioportal-spring-boot
strategy:
rollingUpdate:
maxSurge: 2
maxUnavailable: 1
type: RollingUpdate
template:
metadata:
creationTimestamp: null
labels:
run: cbioportal-spring-boot
spec:
containers:
- envFrom:
- configMapRef:
name: cbioportal-public
image: cbioportal/cbioportal:3.0.6-web-shenandoah-test-oldimage
command: [ "/usr/bin/java" ]
args: [
# from https://developers.redhat.com/blog/2017/04/04/openjdk-and-containers/
"-Xms100m",
"-Xmx25g",
"-XX:+UnlockExperimentalVMOptions",
"-XX:+UseShenandoahGC",
"-XX:ShenandoahUncommitDelay=1000",
"-XX:ShenandoahGuaranteedGCInterval=10000",
#"-XX:+AlwaysPreTouch",
#"-XX:+UseTransparentHugePages",
#"-XX:+UseNUMA",
#"-XX:+PrintGCDetails",
#"-XX:+UseParallelGC",
#"-XX:+PrintGCDateStamps",
#"-XX:ParallelGCThreads=4",
#"-XX:+UseG1GC",
#"-XX:+AggressiveHeap",
# non aggressive garbage collection
#"-XX:MinHeapFreeRatio=20",
#"-XX:MaxHeapFreeRatio=40",
#"-XX:GCTimeRatio=19",
#"-XX:AdaptiveSizePolicyWeight=90",
"-XX:+UseCGroupMemoryLimitForHeap",
# This issue says to use maxRAMFraction > 1
# https://github.com/akka/akka/issues/23499, but haven't found this
# to work v well
#"-XX:MaxRAMFraction=1",
"-XX:+PrintFlagsFinal",
"-XshowSettings:vm",
# need to set MaxRAM, somehow the MaxRAMFraction is not picked up
# from the limits
#"-XX:MaxRAM=6500m",
# enable remote debug
"-Dcom.sun.management.jmxremote.rmi.port=8849",
"-Dcom.sun.management.jmxremote=false",
"-Dcom.sun.management.jmxremote.port=8849",
"-Dcom.sun.management.jmxremote.ssl=false",
"-Dcom.sun.management.jmxremote.authenticate=false",
"-Dcom.sun.management.jmxremote.local.only=false",
"-Djava.rmi.server.hostname=localhost",
# /enable remote debug
"-Dfrontend.url=https://frontend.cbioportal.org",
"-Ddefault_cross_cancer_study_session_id=5c8a7d55e4b046111fee2296",
"-Dquick_search.enabled=true",
"-Dskin.footer=",
"-Dskin.right_nav.whats_new_blurb=",
"-Dskin.quick_select_buttons=TCGA PanCancer Atlas Studies#*pan_can_atlas*;Curated set of non-redundant studies|158 studies that are manually curated including TCGA and non-TCGA studies with no overlapping samples#acbc_mskcc_2015,acc_tcga_pan_can_atlas_2018,acyc_fmi_2014,acyc_mda_2015,acyc_mgh_2016,acyc_mskcc_2013,acyc_sanger_2013,all_phase2_target_2018_pub,all_stjude_2016,aml_target_2018_pub,ampca_bcm_2016,angs_project_painter_2018,bfn_duke_nus_2015,blca_bgi,blca_cornell_2016,blca_dfarber_mskcc_2014,blca_mskcc_solit_2012,blca_mskcc_solit_2014,blca_tcga_pan_can_atlas_2018,brca_bccrc,brca_broad,brca_igr_2015,brca_mbcproject_wagle_2017,brca_metabric,brca_sanger,brca_tcga_pan_can_atlas_2018,ccrcc_irc_2014,ccrcc_utokyo_2013,cesc_tcga_pan_can_atlas_2018,chol_jhu_2013,chol_nccs_2013,chol_nus_2012,chol_tcga_pan_can_atlas_2018,cll_iuopa_2015,cllsll_icgc_2011,coadread_dfci_2016,coadread_genentech,coadread_mskcc,coadread_tcga_pan_can_atlas_2018,cscc_dfarber_2015,cscc_hgsc_bcm_2014,ctcl_columbia_2015,desm_broad_2015,dlbc_tcga_pan_can_atlas_2018,dlbcl_dfci_2018,dlbcl_duke_2017,egc_tmucih_2015,es_dfarber_broad_2014,es_iocurie_2014,esca_broad,esca_tcga_pan_can_atlas_2018,escc_icgc,escc_ucla_2014,gbc_shanghai_2014,gbm_tcga_pan_can_atlas_2018,glioma_msk_2018,hcc_inserm_fr_2015,hcc_msk_venturaa_2018,hnsc_broad,hnsc_jhu,hnsc_mdanderson_2013,hnsc_tcga_pan_can_atlas_2018,kich_tcga_pan_can_atlas_2018,kirc_bgi,kirc_tcga_pan_can_atlas_2018,kirp_tcga_pan_can_atlas_2018,laml_tcga_pan_can_atlas_2018,lcll_broad_2013,lgg_tcga_pan_can_atlas_2018,lgg_ucsf_2014,liad_inserm_fr_2014,lihc_amc_prv,lihc_riken,lihc_tcga_pan_can_atlas_2018,luad_broad,luad_tcga_pan_can_atlas_2018,luad_tsp,lung_msk_pdx,lusc_tcga_pan_can_atlas_2018,mbl_broad_2012,mbl_pcgp,mbl_sickkids_2016,mcl_idibips_2013,mds_tokyo_2011,mel_tsam_liang_2017,meso_tcga_pan_can_atlas_2018,mixed_allen_2018,mixed_pipseq_2017,mm_broad,mpnst_mskcc,mrt_bcgsc_2016,msk_impact_2017,nbl_amc_2012,nbl_target_2018_pub,nbl_ucologne_2015,nccrcc_genentech_2014,nepc_wcm_2016,nhl_bcgsc_2011,nhl_bcgsc_2013,npc_nusingapore,nsclc_unito_2016,ov_tcga_pan_can_atlas_2018,paac_jhu_2014,paad_qcmg_uq_2016,paad_tcga_pan_can_atlas_2018,paad_utsw_2015,pact_jhu_2011,panet_arcnet_2017,panet_jhu_2011,panet_shanghai_2013,pcnsl_mayo_2015,pcpg_tcga_pan_can_atlas_2018,pediatric_dkfz_2017,plmeso_nyu_2015,prad_broad,prad_eururol_2017,prad_fhcrc,prad_mich,prad_mpcproject_2018,prad_mskcc,prad_mskcc_cheny1_organoids_2014,prad_tcga_pan_can_atlas_2018,rms_nih_2014,rt_target_2018_pub,sarc_mskcc,sarc_tcga_pan_can_atlas_2018,scco_mskcc,sclc_cancercell_gardner_2017,sclc_jhu,sclc_ucologne_2015,skcm_broad,skcm_broad_brafresist_2012,skcm_tcga_pan_can_atlas_2018,skcm_ucla_2016,skcm_vanderbilt_mskcc_2015,skcm_yale,stad_pfizer_uhongkong,stad_tcga_pan_can_atlas_2018,stad_utokyo,summit_2018,tet_nci_2014,tgct_tcga_pan_can_atlas_2018,thca_tcga_pan_can_atlas_2018,thym_tcga_pan_can_atlas_2018,uccc_nih_2017,ucec_tcga_pan_can_atlas_2018,ucs_jhu_2014,ucs_tcga_pan_can_atlas_2018,um_qimr_2016,urcc_mskcc_2016,utuc_mskcc_2015,uvm_tcga_pan_can_atlas_2018,vsc_cuk_2018,wt_target_2018_pub,acyc_jhu_2016,histiocytosis_cobi_msk_2019,utuc_cornell_baylor_mdacc_2019,prad_su2c_2019",
"-Dskin.example_study_queries=tcga pancancer atlas\ntcga provisional\ntcga -provisional -pancancer\ntcga or icgc\nmsk-impact\n-\"cell line\"\nbreast\nesophageal OR stomach\nprostate msk\nserous",
"-Dapp.name=public-portal",
# connecting over dbcp
"-Ddbconnector=dbcp",
"-Dauthenticate=social_auth_microsoft,social_auth_google",
"-Dauthorization=false",
"-Ddb.user=$(DB_USER)",
"-Ddb.password=$(DB_PASSWORD)",
"-Ddb.host=$(DB_HOST)",
"-Ddb.portal_db_name=$(DB_PORTAL_DB_NAME)",
"-Dtomcat.catalina.scope=runtime",
"-Ddb.connection_string=$(DB_CONNECTION_STRING)",
"-Dshow.civic=$(SHOW_CIVIC)",
"-Dskin.show_tweet_button=$(SKIN_SHOW_TWEET_BUTTON)",
"-Dskin.email_contact=cbioportal@googlegroups.com",
"-Dskin.data_sets_footer=Data sets of published studies were curated from literature. Data sets of provisional TCGA studies were downloaded from the <a href=\"http://gdac.broadinstitute.org\">Broad Institute Firehose</a> and updated quarterly.",
"-Dskin.data_sets_header=The table below lists the number of available samples per cancer study and data type.",
"-Dskin.authorization_message=Welcome to cBioPortal - sign in with your Google account to store your <a href=\"https://www.cbioportal.org/tutorials#virtual-studies\" target=\"_blank\">virtual studies</a> and <a href=\"https://www.cbioportal.org/tutorials#group-comparison\" target=\"_blank\">groups</a>. This will allow you to access your studies and groups from any computer. Login is optional and not required to access any of the other features of cBioPortal.",
"-Dskin.blurb=",
"-Dpriority_studies=PanCancer Studies#msk_impact_2017,nsclc_tcga_broad_2016,mixed_pipseq_2017;Cell lines#cellline_ccle_broad,cellline_nci60",
"-Dmybatis.cache.enabled=false",
"-Dsession.service.url=https://session-service.cbioportal.org/api/sessions/public_portal/",
"-Dsession.service.origin=*",
"-Dsession.service.user=$(SESSION_SERVICE_USER_NAME)",
"-Dsession.service.password=$(SESSION_SERVICE_USER_PASSWORD)",
"-Dgoogle_analytics_profile_id=$(GOOGLE_ANALYTICS_PROFILE_ID)",
"-Dgoogleplus.consumer.key=$(GOOGLE_PLUS_CONSUMER_KEY)",
"-Dgoogleplus.consumer.secret=$(GOOGLE_PLUS_CONSUMER_SECRET)",
"-Dmicrosoftlive.consumer.key=$(MICROSOFT_LIVE_CONSUMER_KEY)",
"-Dmicrosoftlive.consumer.secret=$(MICROSOFT_LIVE_CONSUMER_SECRET)",
"-Dbitly.url=$(BITLY_URL)",
"-Dbitly.access.token=$(BITLY_ACCESS_TOKEN)",
"-Dsentry.dsn=$(SENTRY_DSN)",
"-Dsentryjs.frontend_project_endpoint=$(SENTRY_FRONTEND_DSN)",
"-Ddb.suppress_schema_version_mismatch_errors=true",
"-Dsitemaps=true",
"-Doncokb.public_api.url=https://oncokb.org/api/v1",
"-Dgenomenexus.url=https://www.genomenexus.org",
"-Dmatchminer.url=http://ec2-54-158-52-176.compute-1.amazonaws.com:5555",
"-Dmatchminer.token=$(MATCHMINER_TOKEN)",
"-jar",
"/webapp-runner.jar",
# this addresses same issue as
# https://github.com/cBioPortal/cbioportal/issues/2328 one needs to
# set this if one doesn't want to forward https -> http -> https
# when logging in through google auth. Somehow this goes over http
# otherwise.
"--proxy-base-url",
"https://www.cbioportal.org",
"--max-threads",
"200",
"--session-store",
"redis",
"--session-store-operation-timeout",
"10000",
# Fix long URL https://github.com/cBioPortal/cbioportal/issues/5836
"-AmaxHttpHeaderSize=16384",
"-AconnectionTimeout=20000",
"--enable-compression",
"--port",
"8888",
"/app.war"
]
imagePullPolicy: Always
readinessProbe:
httpGet:
path: /api/cancer-types
port: 8888
initialDelaySeconds: 45
timeoutSeconds: 1
periodSeconds: 5
failureThreshold: 3
livenessProbe:
httpGet:
path: /
port: 8888
initialDelaySeconds: 90
timeoutSeconds: 1
periodSeconds: 12
failureThreshold: 5
name: cbioportal-spring-boot
ports:
- containerPort: 8888
protocol: TCP
- containerPort: 8849
protocol: TCP
resources:
requests:
cpu: 2000m
memory: 20Gi
limits:
memory: 26Gi
terminationMessagePath: /dev/termination-log
terminationMessagePolicy: File
# run on big memory machine
nodeSelector:
kops.k8s.io/instancegroup: large-mem
dnsPolicy: ClusterFirst
restartPolicy: Always
schedulerName: default-scheduler
securityContext: {}
terminationGracePeriodSeconds: 30
status: {}
---
apiVersion: v1
kind: Service
metadata:
labels:
run: cbioportal-spring-boot
name: cbioportal
selfLink: /api/v1/namespaces/default/services/cbioportal-spring-boot
spec:
ports:
- port: 80
name: http
targetPort: 8888
selector:
run: cbioportal-spring-boot
type: ClusterIP
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