docker-images/docker-compose.remote.yml at master · MbqIIB/docker-images · GitHub

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
version: '2'
services:

  # ORACLE DB tunnel
  oracledb:
    image: thomass/ssh-client
    hostname: ${ORACLEHOST}
    container_name: ${ORACLEHOST}
    volumes:
      - ~/.ssh:/ssh
    command: ssh -Ng -L 1521:${ORACLEHOST}:1521 -i /ssh/${SSH_KEY} -o StrictHostKeyChecking=no ${SSH_HOST}
    networks:
      - i2b2-net
    ports:
      - 1521:1521

  # IRCT DB tunnel
  irctdb:
    image: thomass/ssh-client
    hostname: ${IRCTMYSQLADDRESS}
    container_name: ${IRCTMYSQLADDRESS}
    volumes:
      - ~/.ssh:/ssh
    command: ssh -Ng -L ${IRCT_DB_PORT}:${IRCTMYSQLADDRESS}:${IRCT_DB_PORT} -i /ssh/${SSH_KEY} -o StrictHostKeyChecking=no ${SSH_HOST}
    networks:
      - i2b2-net
    ports:
      - ${IRCT_DB_PORT}:${IRCT_DB_PORT}


  nginx:
    build:
        context: nginx/
    image: dtr.avl.dbmi.hms.harvard.edu/dbmi/nginx:${nginx_version}
    restart: always
    ports:
      - "80:80"
      - "443:443"
    networks:
      - i2b2-net
    depends_on:
      - i2b2transmart
      - irct
      - i2b2-wildfly
      - rserve

  i2b2transmart:
    build:
        context: i2b2transmart/
    image: dtr.avl.dbmi.hms.harvard.edu/dbmi/i2b2transmart:${i2b2transmart_version}
    environment:
      - ORACLEHOST=${ORACLEHOST}
      - DB_PORT=${DB_PORT}
      - DB_USER=${DB_USER}
      - BIOMART_USER=${BIOMART_USER}
      - AUTH0_DOMAIN=${AUTH0_DOMAIN}
      - AUTH0_CLIENT_ID=${AUTH0_CLIENT_ID}
      - AUTH0_CLIENT_SECRET=${AUTH0_CLIENT_SECRET}
      - RSERVE_HOST=rserve
      - RSERVE_PORT=6311
      - JPDA_OPTS="-agentlib:jdwp=transport=dt_socket,address=8000,server=y,suspend=n"
      - JPDA_ADDRESS=8000
      - JPDA_TRANSPORT=dt_socket
    entrypoint: ./bin/catalina.sh jpda run
    restart: always
    depends_on:
      - oracledb
    networks:
      - i2b2-net
    expose:
      - 8080
      - 8000
    ports:
      - 8000:8000
      - 9999:8080
    mem_limit: "2g"
    volumes:
      - ${LOCAL_TRANSMART}:/usr/local/tomcat/webapps/:rw

  i2b2-wildfly:
    build:
        context: i2b2-wildfly/
    image: dtr.avl.dbmi.hms.harvard.edu/dbmi/i2b2-wildfly:${i2b2_wildfly_version}
    environment:
      - ORACLEHOST=${ORACLEHOST}
      - DB_PORT=${DB_PORT}
      - I2B2HIVE=${I2B2HIVE}
      - I2B2DEMODATA=${I2B2DEMODATA}
      - I2B2METADATA=${I2B2METADATA}
      - I2B2PM=${I2B2PM}
      - I2B2WORKDATA=${I2B2WORKDATA}
    restart: always
    networks:
      - i2b2-net
    expose:
      - 9090
    ports:
      - 9090:9090

  rserve:
    build:
        context: rserve/
    image: dtr.avl.dbmi.hms.harvard.edu/dbmi/rserve:${rserve_version}
    restart: always
    expose:
      - 6311
    ports:
      - 6311:6311
    networks:
      - i2b2-net

  irct:
    build:
        context: irct/
    image: dtr.avl.dbmi.hms.harvard.edu/dbmi/irct:${irct_version}
    depends_on:
       - irctdb
    environment:
      - IRCTMYSQLADDRESS=${IRCTMYSQLADDRESS}
      - IRCT_DB_PORT=${IRCT_DB_PORT}
      - IRCT_DB_CONNECTION_USER=${IRCT_DB_CONNECTION_USER}
      - IRCTMYSQLPASS=${IRCTMYSQLPASS}
      - AUTH0_DOMAIN=${AUTH0_DOMAIN}
      - AUTH0_CLIENT_ID=${AUTH0_CLIENT_ID}
      - AUTH0_CLIENT_SECRET=${AUTH0_CLIENT_SECRET}
    command: --debug --server-config=standalone.xml
    restart: always
    networks:
      - i2b2-net
    expose:
      - 8080
      - 8787
    ports:
      - 8080:8080
      - 8787:8787


networks:
    i2b2-net: