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This note describes installation of tranSMART version 16.2, released on 6 Feb 2017 (installed on Ubuntu 14.04)

Discussion on upgrading to 16.2 from an earlier version can be found here.

Table of Contents

Overview

...

  • Create a folder, transmart, to contain the app, scripts, and data

  • Within that folder, using curl, download https://github.com/tranSMART-Foundation/transmart-data/archive/release-16.2.zip
  • Expand that zip file into ~/transmart/transmart-data
  • Within that folder run the initial setup commands (these instructions are basically from the file ~/transmart/transmart-data/README.md)
  • Run additional commands to install ant and maven

 


Code Block
languagebash
themeMidnight
mkdir ~/transmart
cd ~/transmart
sudo apt-get install -y curl
curl http://library.transmartfoundation.org/release/release16_2_0_artifacts/transmart-data-release-16.2.zip -o transmart-data-release-16.2.zip
unzip transmart-data-release-16.2.zip
mv transmart-data-release-16.2 transmart-data
cd transmart-data
sudo make -C env ubuntu_deps_root
make -C env ubuntu_deps_regular
sudo apt-get install -y ant
sudo apt-get install -y maven

...

Expand
titleOther Operating Systems - Click here to expand...

The command-line artifacts loaded in this section are required for the scripts that follow. They are the following: postgresql make git rsync libcairo-dev php5-cli php5-json curl tar openjdk-7-jdk zip unzip

In addition, to compile R from source code you will need: gfortran g++ libreadline-dev libxt-dev libpango1.0-dev libprotoc-dev texlive-fonts-recommended tex-gyre liblz4-tool pv

On Mac OsX the native version of tar does not work, you need gnutar instead.

 


Install Grails 2.x

This step will install Grails and Groovy - https://grails.org/download.html - also see http://grails.org/doc/latest/guide/gettingStarted.html

...

Code Block
languagebash
themeMidnight
cd ~
echo "export PATH=${HOME}/transmart/transmart-data/R/root/bin:$PATH" > Rpath.sh
sudo mv Rpath.sh /etc/profile.d/

 


This change will take place when you next start the machine, login, or start a new terminal window or shell. To have them take effect immediately you must:

...

ls /var/lib/postgresql/tablespaces

In addition, those install steps start PostgreSQL and set init files so that PostgreSQL will start on OS restart and after reboot.

This means that there is a postgresql service to start/stop and get status of PostgreSQL, specifically, 

sudo service postgresql start
sudo service postgresql stop
sudo service postgresql status 

Using the R Interface (Optional)

Follow the instructions in the README.md file at this location:

https://github.com/tranSMART-Foundation/RInterface/tree/release-16.2

FAQs

 


Expand
titleAfter initially installing tranSMART, how do I confirm that it works ?

Start with the Sanity Checklist. If that is successful, you can work through the exercises provided in the user guide.

Expand
titleWhat security group setting should I use?

The security group settings should be determined based on the level of access to the data in the system that you want the users and the developers/administrators to have. Here are some suggestions:

Users:

  • Open HTTP to the IP address range for the users or make it accessible to the world (i.e. 0.0.0.0/0)

Developers/Administrators:

  • Open SSH to putty or ssh into the box
  • Open 8080 for testing of the tomcat-installed application; or the port for HTTP access of your installation
  • Open 8983 so you can access the Solr Admin
  • Normally the DB ports are used only locally (on the Application server for a single host solution; or between App and DB servers for a multiple host solution); for development these may need to be opened - for SSH tunneling, for example.

You can use a band of IPs if you are unable to get an exact IP address.

Anchor
credits
credits
Credits

These install instructions rely on a number of contributions from multiple authors. The various make files in the transmart-data repository were originally written by Gustavo dos Santos Lopes (and teammates) at theHyve; later modified by him, Peter Rice (at Imperial College London) and Ruslan Forostianov (theHyve). In addition, instructions on earlier versions of this wiki, from which these instructions draw heavily, were written by Ruslan Forostianov, Janneke Schoots - van der Ploeg, Jan Kanis, Gustavo dos Santos Lopes, and Ward Weistra (from theHyve), with additional contributions from Zach Wright (University of Michigan), Jinlei Liu (ConvergeHealth by Deloitte), Dave John (while at ConvergeHEALTH by Deloitte), Vasudeva Mahavisno (while at University of Michigan), and Terry Weymouth (University of Michigan).