Name: transmartAppInstaller
Owner: TranSMART Project
Description: Installation script for transmartApp and i2b2 using GAnt (Ant in Groovy)
Created: 2013-06-26 10:33:47.0
Updated: 2013-11-12 21:55:42.0
Pushed: 2013-11-12 21:55:40.0
Homepage: null
Size: 7719
Language: Shell
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transmartAppInstaller meant for tranSMART - translational medicine data mart Author : Pieter Lukasse (pieter at thehyve.nl)
transmartAppInstaller is an installation script that sets up some dependencies for running Postgres-based branches of transmartApp. This includes the tranSMART Postgres database schemas and example content, the database schema and patches for i2b2 (unless you are running the core integration branch, in which case you don't need i2b2), and the tranSMART configuration files. The target audience for this installer is developers who want to experiment with or contribute to Postgres based branches of tranSMART. It is not meant to set up a full production setup of tranSMART.
This software is licensed under the Apache License 2.0. Open source components contained therein may have different (but generally compatible) licenses like Apache License 1.1.
This will set you up with the neccessary database schemas, patch i2b2 so that it runs on Postgres and create the tranSMART configuration files. You will still have to checkout and run transmartApp itself and run JBoss with i2b2 in order to actually get a working tranSMART application. You will probably also need to install R (including Rserve and some other packages) and Solr. How to do this will vary accordingly to the platform and is not handled by this script.
The database settings are a common source of trouble. Explaining the details of PostgreSQL authentication is outside the scope of this document, but I'll leave here general remarks. For more information, see:
You will need a server running on the same machine (if the database is a remote machine, you will have to create the tablespace locations ? but not the tablespaces themselves ? used by the tranSMART database and then you'll have to patch the gant file to skip the creation of those directories in the local machine). You will also need a postgres role with superuser privileges.
In distributions such as Debian or Ubuntu, a superuser role with the name 'postgres' is automatically created. A system user with the same name is also automatically created. In the default setup, this system user can login automatically as DB superuser if it connects to the database using unix sockets. The install script supports this setup by attempting to use 'sudo' in order to login as the 'postgres' user and hence have DB superuser privileges to run the SQL install scripts and commands.
On Mac OSX, I'm told the brew package manager will create a DB superuser with the same name as the installing user, but not a database. In that case, you will only have to setup the workingdb property to something like 'template1' and you can leave the other database settings empty.
Finally, on Windows the postgres user password is asked upon installation. You will have to provide the password to the script and use the db user 'postgres'.