-
Notifications
You must be signed in to change notification settings - Fork 0
/
docker-compose.yml
279 lines (262 loc) · 7.82 KB
/
docker-compose.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
version: '3'
services:
neo4j:
image: neo4j:4.4.7
ports:
# - 7474:7474
- 7687:7687
expose:
- 7474
environment:
- NEO4J_AUTH=neo4j/letmein
- NEO4J_dbms_security_procedures_unrestricted=apoc.*
- NEO4J_apoc_import_file_enabled=true
- NEO4J_apoc_export_file_enabled=true
- NEO4J_dbms_shell_enabled=true
# - NEO4JLABS_PLUGINS=["apoc", "graph-data-science"]
- NEO4J_apoc_import_file_use__neo4j__config=true
volumes:
# - pibu_neo4j_volume:/var/lib/neo4j/data
- ./neo4j/plugins:/var/lib/neo4j/plugins
- ./neo4j/import:/var/lib/neo4j/import
- ./neo4j/data:/var/lib/neo4j/data
# - ./api/src/cql/neo4j.conf:/var/lib/neo4j/conf/neo4j.conf
api:
# For non-M1 machines: comment out arm64v8 and platform field
# image: arm64v8/node:16
# platform: linux/arm64/v8
image: node:16
working_dir: /usr/src/service
command: >
sh -c "node api/src/proxy_pass minio 9000 &
npm run start:api"
expose:
- 4001
ports:
- 9231:9231
environment:
# - NEO4J_URI=bolt://neo4j:7687
- NEO4J_URI=${NEO4J_URI}
- NEO4J_USER=${NEO4J_USER}
- NEO4J_PASSWORD=${NEO4J_PASSWORD}
- GRAPHQL_LISTEN_PORT=${GRAPHQL_SERVER_PORT}
- GRAPHQL_URI=${GRAPHQL_URI}
# Default is 2gb (garbage collection heap memory)
- NODE_OPTIONS=--max_old_space_size=4096
links:
- neo4j
depends_on:
- neo4j
- minio
- keycloak
volumes:
- .:/usr/src/service
- pibu_api_volume:/pibu_data
ui:
# For non-M1 machines: comment out arm64v8 and platform field
image: node:16
# image: arm64v8/node:16
# platform: linux/arm64/v8
working_dir: /usr/src/service
command: >
sh -c "npm run start:ui"
ports:
- 3001:3001
environment:
- CI=true
- REACT_APP_GRAPHQL_URI=${GRAPHQL_SERVER_PATH}
- PROXY=${GRAPHQL_URI}
- NODE_OPTIONS=--max_old_space_size=4096
links:
- api
depends_on:
- api
- minio
- keycloak
volumes:
- .:/usr/src/service
minio:
image: minio/minio:RELEASE.2022-07-30T05-21-40Z
expose:
- ${MINIO_CONSOLE_PORT}
ports:
- ${MINIO_API_PORT}:${MINIO_API_PORT}
volumes:
- pibu_minio_volume:/data
# - /etc/localtime:/etc/localtime:ro
- ~/etc/timezone:/etc/localtime:ro
environment:
- MINIO_ROOT_USER=${MINIO_ROOT_USER}
- MINIO_ROOT_PASSWORD=${MINIO_ROOT_PASSWORD}
command: server /data --console-address ":${MINIO_CONSOLE_PORT}"
keycloak:
# For non-M1 machines: use keycloak 11
# image: jboss/keycloak:11.0.1
image: jboss/keycloak:16.1.1
# image: wizzn/keycloak:12
container_name: keycloak
expose:
- 8443
- 8080
# ports:
# - "8085:8443"
# - "8080:8080"
volumes:
- ./keycloak/realm-export.json:/opt/jboss/keycloak/realm-export.json
- pibu_keycloak_volume:/opt/jboss/keycloak/standalone/data
- ./nginx/certs/bundle.crt:/etc/x509/https/tls.crt
- ./nginx/certs/bundle.key:/etc/x509/https/tls.key
# depends_on:
# - mariadb
# environment:
# - KEYCLOAK_USER=${KEYCLOAK_USER}
# - KEYCLOAK_PASSWORD=${KEYCLOAK_PASSWORD}
# - KEYCLOAK_IMPORT=/opt/jboss/keycloak/realm-export.json
# # - DB_VENDOR=mariadb
# - DB_VENDOR=h2
# - PROXY_ADDRESS_FORWARDING=true
# - REDIRECT_SOCKET="proxy-https"
# - KEYCLOAK_FRONTEND_URL=https://${KEYCLOAK_SERVER_HOST_AND_PORT}/auth
# - DB_ADDR=${KEYCLOAK_DB_ADDR}
# - DB_PORT=${KEYCLOAK_DB_PORT}
# - DB_DATABASE=${KEYCLOAK_DB_DATABASE}
# - DB_USER=${KEYCLOAK_DB_USER}
# - DB_PASSWORD=${KEYCLOAK_DB_PASSWORD}
environment:
- KEYCLOAK_USER=${KEYCLOAK_USER}
- KEYCLOAK_PASSWORD=${KEYCLOAK_PASSWORD}
- KEYCLOAK_IMPORT=/opt/jboss/keycloak/realm-export.json
- DB_VENDOR=h2
- PROXY_ADDRESS_FORWARDING=true
- REDIRECT_SOCKET="proxy-https"
- KEYCLOAK_FRONTEND_URL=https://${KEYCLOAK_SERVER_HOST_AND_PORT}/auth
# funnel:
# image: ohsucompbio/funnel-dind
# container_name: funnel
# privileged: true
# # command: funnel server run --Server.HTTPPort 8003 --Server.RPCPort 9093 --config /opt/funnel/funnel/funnel_config.yaml
# entrypoint: funnel server run --Server.HTTPPort 8003 --Server.RPCPort 9093 --config /opt/funnel/funnel/funnel_config.yaml
# expose:
# - 8003
# - 9093
# # ports:
# # # - 8003:8003
# # - 9093:9093
# depends_on:
# - mongo
# volumes:
# - ./api/src/funnel:/opt/funnel/funnel
# - .:/opt/funnel/service
# - /var/run/docker.sock:/var/run/docker.sock
nginx:
restart: ${RESTART}
build:
context: .
args:
GITLAB_AUTH_TOKEN: ${GITLAB_AUTH_TOKEN}
environment:
- NODE_ENV=production
ports:
- "80:80"
- "443:443"
depends_on:
- api
- minio
- neo4j
- keycloak
volumes:
- ./nginx/conf.d:/etc/nginx/conf.d
- ./nginx/nginx.conf:/etc/nginx/nginx.conf
- ./nginx/certs:/etc/nginx/certs
entrypoint: >
nginx -g "daemon off;"
# graphene:
# image: crescentdev/graphene
# privileged: true
# # build: graphene
# container_name: graphene
# expose:
# - ${GRAPHENE_PORT}
# ports:
# - "${GRAPHENE_PORT}:${GRAPHENE_PORT}"
# environment:
# - MINIO_HOST_PORT=${MINIO_HOST_PORT}
# - MINIO_ACCESS_KEY=${MINIO_ACCESS_KEY}
# - MINIO_SECRET_KEY=${MINIO_SECRET_KEY}
# - MONGO_URL=${MONGO_URL}
# - WES_PORT=${WES_PORT}
# - WES_SERVER=${WES_SERVER}
# - GRAPHENE_DEV=${GRAPHENE_DEV}
# volumes:
# - ./graphene/src:/app/src
# - ./minio:/app/minio
# - ./crescent:/app/crescent
# working_dir: /app/src
# depends_on:
# - minio
# - mongo
# command: uvicorn main:app --host 0.0.0.0 --port ${GRAPHENE_PORT} --reload
# wes-server:
# build: wes
# # image: kevin/wes-server
# container_name: "wes-server"
# volumes:
# - /var/run/docker.sock:/var/run/docker.sock:rw
# - /var/lib/docker/volumes:/var/lib/docker/volumes:rw
# - /tmp:/tmp:rw
# - /var/lib/toil:/var/lib/toil:rw
# - ./wes/workflows:/root/workflows:rw
# - ./wes/logs:/root/logs:rw
# ports:
# - "${WES_PORT}:8081"
# environment:
# - MINIO_HOST_PORT=${MINIO_HOST_PORT}
# - MINIO_ACCESS_KEY=${MINIO_ACCESS_KEY}
# - MINIO_SECRET_KEY=${MINIO_SECRET_KEY}
# entrypoint: /root/mesos-wes.sh
# command:
# - --port=8081
# - --backend=${WES_BACKEND}
# - --opt=runner=${WES_CWL_RUNNER}
# - --opt=extra=--cleanWorkDir=never
# - --opt=extra=--writeLogs=/root/logs
# - --opt=extra=--writeLogsFromAllJobs
# - --opt=extra=--maxLogFileSize=0
# - --opt=extra=--realTimeLogging
# - --opt=extra=--retryCount=0
# mongo:
# image: mongo:5.0.17
# ports:
# - "27017:27017"
# # environment:
# # - MONGO_INITDB_ROOT_USERNAME=mongoadmin
# # - MONGO_INITDB_ROOT_PASSWORD=mongoadmin
# volumes:
# - pibu_mongo_volume:/data/db
# # - /etc/localtime:/etc/localtime:ro
# - ~/etc/timezone:/etc/localtime:ro
# # - ./mongo-entrypoint/:/docker-entrypoint-initdb.d/
# mariadb:
# image: mariadb:10.7.8
# environment:
# MYSQL_ROOT_PASSWORD: ${MARIADB_ROOT_PASSWORD}
# MYSQL_DATABASE: ${KEYCLOAK_DB_DATABASE}
# MYSQL_USER: ${KEYCLOAK_DB_USER}
# MYSQL_PASSWORD: ${KEYCLOAK_DB_PASSWORD}
# volumes:
# - pibu_mariadb_volume:/var/lib/mysql
# ports:
# - "3306:3306"
volumes:
pibu_minio_volume:
external: true
pibu_keycloak_volume:
external: true
pibu_api_volume:
external: true
pibu_neo4j_volume:
external: true
pibu_mongo_volume:
external: true
pibu_mariadb_volume:
external: true