Updated readme

README.md

 # Phenotips Docker Image
 > Contains CHGI ldap bindings in the example config directory.
 
-
-
 ## Docker-compose
-To integrate with the gene42 docker-compose.yml file, modify to match:
+Use the following compose file to set up a clean installation of PhenoTips. The config directory should contain the example configs in this project. All other volume directories can be empty. 
+
 ```
-  staging_phenotips:
-    container_name: staging_phenotips
+version: '3.3'
+
+services:
+  phenotips:
     image: docker.ucalgary.ca/lleung/chgi-phenotips:1.4.7
-    restart: always
-    networks:
-      - staging_web
-      - staging_backend
     expose:
       - 8080
+    ports:
+      - "136.159.169.156:8080:8080"
+    networks:
+      - dbnet
+    volumes:
+      - /root/docker/phenotips/_data:/var/lib/phenotips
+      - /root/docker/config:/config
+      - /root/docker/logs/_data:/var/local/tomcat/logs
+
+  db:
+    image: mariadb:10
     volumes:
-      - staging_phenotips_local-storage_persistent:/var/lib/phenotips
-      - /local/lib/docker/volumes/staging_phenotips_config/_data/conf/WEB-INF/:/config
-      - staging_phenotips_logs_persistent:/var/local/tomcat/logs
+      - /root/docker/database:/var/lib/mysql
+    environment:
+      - MYSQL_ROOT_PASSWORD=phenotips
+      - MYSQL_DATABASE=phenotips
+      - MYSQL_USER=phenotips
+      - MYSQL_PASSWORD=phenotips
+    # command: mysqld --innodb-buffer-pool-size=768M --max_allowed_packet=128M # --skip-grant-tables
+    networks:
+      - dbnet
+    restart: always
+
+networks:
+  dbnet:
+
+```
+
+# Todo
+## Root Container
+Not sure if root is required. Would be nice to add:
+```
     cap_drop:
       - SYS_ADMIN
-    environment:
-    - JAVA_HEAP=3096m
-    - JAVA_OPTS=
 ```
+
+
+