wiki:i2b2 HowTo Install Using Docker

Please read Docker HowTo Install before installing i2b2

Prerequisites if required

Step 1 - Install Docker

Docker HowTo Install

Step 2 - Install Git

$ sudo apt-get update

$ sudo apt-get install git

Install using Docker

This will install i2b2 1.7.08

  1. On the host machine go to directory

/local/docker/<USER>/

  1. Go to this directory and checkout from git docker_i2b2_1708_fresh

sudo git clone https://github.com/LCBRU/docker_i2b2_1708_fresh.git

sudo chmod -R 777 docker_i2b2_1708_fresh/

A README.md file is available here.

This will create a directory /local/docker/<USER>/docker_i2b2_1708_fresh

  1. Go to the folder 'scripts' and view the file CreateDatabase.sql

Run these on your Microsoft sql database only if you are creating a new i2b2 install.

  1. The main configuration files are :

i2b2-1.7.08-install-procedures/config/config.properties

i2b2-1.7.08-install-procedures/config/defaults.sh

i2b2-1.7.08-install-procedures/bin/compositions/install-all.sh

  1. In the file install-all.sh, make sure that you comment out the line :

# $I2B2_INSTALL_PROCS_HOME/bin/installs/6-data-install.sh $JOB_NAME

also look at files in the folder :

docker_i2b2_1708_fresh/i2b2-1.7.08-install-procedures/merge-files/sqlserver/data/sql

If you have a fresh database uncomment it.

  1. Modify the following files :

docker_i2b2_1708_fresh/www/admin/i2b2_config_data.js

docker_i2b2_1708_fresh/www/main/i2b2_config_data.js

docker_i2b2_1708_fresh/www/webclient/i2b2_config_data.js

Make sure urlCellPM contains the correct server i.e. "http://uhlbriccsapp03.xuhl-tr.nhs.uk

  1. Build Docker container

sudo docker build -t lcbruit/i2b2:v1.7.08 .

  1. Run container

sudo docker run -v /share:/share -itd -p 80:80 -p 8080:8080 -p 9990:9990 -p 9090:9090 lcbruit/i2b2:v1.7.08

  1. Open URL

http://<HOST>.xuhl-tr.nhs.uk/admin

http://<HOST>.xuhl-tr.nhs.uk/main

http://<HOST>.xuhl-tr.nhs.uk/webclient

  1. Use the following to connect to server :

sudo docker ps -a

sudo docker exec -i -t [CONTAINER ID] /bin/bash

  1. To stop and start tomcat use :

/i2b2/jboss/bin/jboss-cli.sh --connect command=:shutdown

/i2b2/jboss/bin/standalone.sh -b 0.0.0.0

Useful locations

https://github.com/LCBRU/docker_i2b2_1708_fresh/tree/master/datasources

https://github.com/LCBRU/docker_i2b2_1708_fresh/tree/master/i2b2-1.7.08-install-procedures/merge-files/sqlserver/data/sql

Last modified 6 years ago Last modified on 03/23/17 15:18:46
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