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chore: disable node 2 for now
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@davidlougheed
davidlougheed committed Jan 9, 2024
1 parent 8a33806 commit 9d3408b
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Showing 3 changed files with 76 additions and 65 deletions.
123 changes: 67 additions & 56 deletions epivar-prod/docker-compose.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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

# --------------------------------------------------------------------------------------------------------------------

Expand All @@ -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
16 changes: 8 additions & 8 deletions epivar-prod/nginx.conf
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
# }
}
2 changes: 1 addition & 1 deletion epivar-prod/portal.env
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Original file line number Diff line number Diff line change
@@ -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

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