move docker compose files over to diff repo

README.md

-# cbioportal-docker-compose
-Run cBioPortal using Docker Compose
+# Run cBioPortal using Docker Compose
+Download necessary files (seed data, example config and example study from
+datahub):
+```
+./init.sh
+```
+
+Start docker containers. This can take a few minutes the first time because the
+database needs to import some data.
+```
+docker-compose up
+```
+In a different terminal import a study
+```
+docker-compose run cbioportal metaImport.py -u http://cbioportal:8080 -s study/lgg_ucsf_2014/ -o
+```

config/init.sh

+#!/usr/bin/env bash
+
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+
+docker run --rm -it cbioportal/cbioportal:3.4.4 cat /cbioportal-webapp/WEB-INF/classes/portal.properties | \
+    sed 's/db.host=.*/db.host=cbioportal_database:3306/g' | \
+    sed 's|db.connection_string=.*|db.connection_string=jdbc:mysql://cbioportal_database:3306/|g' \
+> portal.properties

data/init.sh

+# Download the seed database
+wget -O cgds.sql "https://raw.githubusercontent.com/cBioPortal/cbioportal/v2.0.0/db-scripts/src/main/resources/cgds.sql" && wget -O seed-cbioportal_hg19_v2.7.3.sql.gz "https://github.com/cBioPortal/datahub/raw/master/seedDB/seed-cbioportal_hg19_v2.7.3.sql.gz"

docker-compose.yml

+version: '3'
+
+services:
+  cbioportal:
+    restart: unless-stopped
+    image: inodb/cbioportal:docker-compose-layer
+    container_name: cbioportal_container
+    environment:
+      SHOW_DEBUG_INFO: "true"
+    ports:
+      - "8080:8080"
+    volumes:
+     - ./study:/study/
+     - ./config/portal.properties:/cbioportal/portal.properties:ro
+    depends_on:
+     - cbioportal_database
+     - cbioportal_session
+    networks:
+     - cbio-net
+    command: /bin/sh -c "java -Xms2g -Xmx4g -Dauthenticate=noauthsessionservice -Dsession.service.url=http://cbioportal_session:5000/api/sessions/my_portal/ -jar webapp-runner.jar /cbioportal-webapp"
+  cbioportal_database:
+    restart: unless-stopped
+    image: mysql:5.7
+    container_name: cbioportal_database_container
+    environment:
+      MYSQL_DATABASE: cbioportal
+      MYSQL_USER: cbio_user
+      MYSQL_PASSWORD: somepassword
+      MYSQL_ROOT_PASSWORD: somepassword
+    volumes:
+     - ./data/cgds.sql:/docker-entrypoint-initdb.d/cgds.sql:ro
+     - ./data/seed-cbioportal_hg19_v2.7.3.sql.gz:/docker-entrypoint-initdb.d/seed.sql.gz:ro
+     - cbioportal_mysql_data:/var/lib/mysql
+    networks:
+     - cbio-net
+  cbioportal_session:
+    restart: unless-stopped
+    image: cbioportal/session-service:0.2.0
+    container_name: cbioportal_session_container
+    environment:
+      SERVER_PORT: 5000
+      JAVA_OPTS: -Dspring.data.mongodb.uri=mongodb://cbioportal_session_database:27017/session-service
+    depends_on:
+      - cbioportal_session_database
+    networks:
+      - cbio-net
+  cbioportal_session_database:
+    restart: unless-stopped
+    image: mongo:3.7.9
+    container_name: cbioportal_session_database_container
+    environment:
+      MONGO_INITDB_DATABASE: session_service
+    volumes:
+      - cbioportal_mongo_data:/data/db
+    networks:
+      - cbio-net
+
+networks:
+  cbio-net: 
+  
+volumes:
+  cbioportal_mysql_data:
+  cbioportal_mongo_data:

init.sh

+#!/usr/bin/env bash
+for d in config data study; do
+    cd $d; ./init.sh
+    cd ..
+done

study/init.sh

+#!/usr/bin/env bash
+# download data hub study and import
+
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+
+DATAHUB_STUDIES="${DATAHUB_STUDIES:-lgg_ucsf_2014}"
+for study in ${DATAHUB_STUDIES}; do
+    mkdir -p ${study} && \
+        cd ${study} && \
+        wget -O ${study}.tar.gz "http://download.cbioportal.org/${study}.tar.gz"
+        tar xvfz ${study}.tar.gz
+done