diff --git a/epivar-prod/docker-compose.yml b/epivar-prod/docker-compose.yml index 6756599c..7188a209 100644 --- a/epivar-prod/docker-compose.yml +++ b/epivar-prod/docker-compose.yml @@ -8,11 +8,11 @@ services: depends_on: - epivar-portal - epivar-node-1-server - - epivar-node-2-server +# - epivar-node-2-server networks: - epivar-portal-net - epivar-node-1-server-net - - epivar-node-2-server-net +# - epivar-node-2-server-net epivar-portal: user: $USER:$USER @@ -47,6 +47,9 @@ services: # genotypes: VCF + index file - /flu-infection-data/node1/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.vcf.gz:/app/data/genotypes.vcf.gz:ro - /flu-infection-data/node1/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.vcf.gz.tbi:/app/data/genotypes.vcf.gz.tbi:ro + # peaks files + - /flu-infection-data/node1/matrices:/app/input-files/matrices:ro + - /flu-infection-data/node1/qtls:/app/input-files/qtls:ro # tracks: # - metadata JSON file, - node1/metadata.json:/app/data/metadata.json:ro @@ -76,51 +79,59 @@ services: # Node 2: hg38 data (lifted over) ------------------------------------------------------------------------------------ - epivar-node-2-server: - user: $USER:$USER - image: ghcr.io/c3g/epivar-server:latest - networks: - - epivar-node-2-server-net - - epivar-node-2-redis-net - - epivar-node-2-db-net - depends_on: - - epivar-node-2-redis - - epivar-node-2-db - env_file: - - node2/secrets.env - environment: - - NODE_ENV=production - - EPIVAR_REDIS_CONNECTION=redis://epivar-node-2-redis:6379 - - EPIVAR_IMPORT_MAX_P_VAL=0.05 - - EPIVAR_LOW_COUNT_THRESHOLD=5 - volumes: - # dataset configuration: about Markdown file, EpiVar config.js, tracks metadata.json - - node2/about.md:/app/data/about.md - - node2/config.js:/app/config.js:ro - # genotypes: VCF + index file - - /flu-infection-data/node2/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.vcf.gz:/app/data/genotypes.vcf.gz:ro - - /flu-infection-data/node2/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.vcf.gz.tbi:/app/data/genotypes.vcf.gz.tbi:ro - # tracks: metadata JSON file, sample bigWigs and writeable volume for on-the-fly merged tracks - - node2/metadata.json:/app/data/metadata.json:ro - - /flu-infection-data/node2/tracks:/tracks:ro - - /flu-infection-data/node2/mergedTracks:/mergedTracks - - epivar-node-2-redis: - image: redis:7.2 - networks: - - epivar-node-2-redis-net - volumes: - - /opt/epivar/node2/redis:/data - - epivar-node-2-db: - image: postgres:15 - networks: - - epivar-node-2-db-net - env_file: - - node2/secrets.env - volumes: - - node2/postgresql.conf:/etc/postgresql/postgresql.conf:ro - - /opt/epivar/node2/db:/var/lib/postgresql/data + # epivar-node-2-server: + # user: $USER:$USER + # image: ghcr.io/c3g/epivar-server:latest + # networks: + # - epivar-node-2-server-net + # - epivar-node-2-redis-net + # - epivar-node-2-db-net + # depends_on: + # - epivar-node-2-redis + # - epivar-node-2-db + # env_file: + # - node2/secrets.env + # environment: + # - NODE_ENV=production + # - EPIVAR_REDIS_CONNECTION=redis://epivar-node-2-redis:6379 + # - EPIVAR_IMPORT_MAX_P_VAL=0.05 + # - EPIVAR_LOW_COUNT_THRESHOLD=5 + # volumes: + # # dataset configuration: about Markdown file, EpiVar config.js, tracks metadata.json + # - node2/about.md:/app/data/about.md + # - node2/config.js:/app/config.js:ro + # # genotypes: VCF + index file + # - /flu-infection-data/node2/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.GRCh38.vcf.gz:/app/data/genotypes.vcf.gz:ro + # - /flu-infection-data/node2/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.GRCh38.vcf.gz.tbi:/app/data/genotypes.vcf.gz.tbi:ro + # # peaks files + # - /flu-infection-data/node2/matrices:/app/input-files/matrices:ro + # - /flu-infection-data/node2/qtls:/app/input-files/qtls:ro + # # tracks: + # # - metadata JSON file, + # - node1/metadata.json:/app/data/metadata.json:ro + # # - sample bigWigs, + # - /flu-infection-data/node1/tracks:/tracks:ro + # # - writeable volume for on-the-fly merged tracks, + # - /flu-infection-data/node1/mergedTracks:/mergedTracks + # # - other static tracks for showing in the UCSC browser. + # # *** NONE FOR NODE 2 *** + # + # epivar-node-2-redis: + # image: redis:7.2 + # networks: + # - epivar-node-2-redis-net + # volumes: + # - /opt/epivar/node2/redis:/data + # + # epivar-node-2-db: + # image: postgres:15 + # networks: + # - epivar-node-2-db-net + # env_file: + # - node2/secrets.env + # volumes: + # - node2/postgresql.conf:/etc/postgresql/postgresql.conf:ro + # - /opt/epivar/node2/db:/var/lib/postgresql/data # -------------------------------------------------------------------------------------------------------------------- @@ -139,12 +150,12 @@ networks: driver: bridge internal: true - epivar-node-2-server-net: - driver: bridge - internal: true - epivar-node-2-redis-net: - driver: bridge - internal: true - epivar-node-2-db-net: - driver: bridge - internal: true +# epivar-node-2-server-net: +# driver: bridge +# internal: true +# epivar-node-2-redis-net: +# driver: bridge +# internal: true +# epivar-node-2-db-net: +# driver: bridge +# internal: true diff --git a/epivar-prod/nginx.conf b/epivar-prod/nginx.conf index b2ff5ebe..605f22c8 100644 --- a/epivar-prod/nginx.conf +++ b/epivar-prod/nginx.conf @@ -46,12 +46,12 @@ server { proxy_pass http://epivar-node-1-server:3002; } - location /aracena-hg38/api/ { - proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; # Legacy, replaced by Forwarded - proxy_set_header X-Real-IP $remote_addr; - proxy_set_header Host $http_host; - proxy_set_header Forwarded "$proxy_add_forwarded;proto=$scheme"; - - proxy_pass http://epivar-node-2-server:3002; - } +# location /aracena-hg38/api/ { +# proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; # Legacy, replaced by Forwarded +# proxy_set_header X-Real-IP $remote_addr; +# proxy_set_header Host $http_host; +# proxy_set_header Forwarded "$proxy_add_forwarded;proto=$scheme"; +# +# proxy_pass http://epivar-node-2-server:3002; +# } } diff --git a/epivar-prod/portal.env b/epivar-prod/portal.env index fd6ed980..164b4a0f 100644 --- a/epivar-prod/portal.env +++ b/epivar-prod/portal.env @@ -1 +1 @@ -EPIVAR_NODES='https://flu-infection.vhost38.genap.ca/aracena-hg19;https://flu-infection.vhost38.genap.ca/aracena-hg38' +EPIVAR_NODES=https://flu-infection.vhost38.genap.ca/aracena-hg19