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This note describes installation of tranSMART version 16.23, released on 6 Feb 2017 August 2018 (installed on Ubuntu 1416.04)

Discussion on upgrading to 16.2 3 from an earlier version can be found here.

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These instructions are based on the assumption that you are installing tranSMART version 16.2 3 on Ubuntu 14.04. They draw heavily on previous versions of the release notes, see the credits section of this document for details.

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Code Block
languagebash
themeMidnight
titleDownload, install Scripts
sudo apt-get install -y curl
sudo apt-get install -y unzip 

# download the installation script
curl http://library.transmartfoundation.org/release/release16_23_0_artifacts/Scripts-release-16.23.zip -o Scripts-release-16.23.zip
# unzip and rename the Scripts folder
unzip Scripts-release-16.23.zip
mv Scripts-release-16.23 Scripts

Run the install script

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In these instructions, you will be download the tranSMART release artifacts from the tranSMART library. The current release is tranSMART release 16.23, and it is visible in the library at http://library.transmartfoundation.org/release/release16_23_0.html. As you can see from that page, the artifacts are presented as either zip or war files and each has a PGP signed "detached signature", and files containing the MD5 hash and a SHA1 hash. These can be used to verify the file being download. The process for verification is covered separately. 

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  • 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-16.23.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

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Code Block
languagebash
themeMidnight
mkdir ~/transmart
cd ~/transmart
sudo apt-get install -y curl
curl http://library.transmartfoundation.org/release/release16_23_0_artifacts/transmart-data-release-16.23.zip -o transmart-data-release-16.23.zip
unzip transmart-data-release-16.23.zip
mv transmart-data-release-16.23 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

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From the transmart-library web site, download the application's war files: transmart.v16.23.war and gwava.v16.23.war. We will copy then to a staging directory at ~/transmart/war-files . And then, install then in tomcat's webapps directory as transmart.war and gwava.war. Specifically,

Code Block
languagebash
themeMidnight
cd ~/transmart
mkdir war-files
cd war-files
curl http://library.transmartfoundation.org/release/release16_23_0_artifacts/transmart.war --output transmart.war
curl http://library.transmartfoundation.org/release/release16_23_0_artifacts/gwava.war--output gwava.war
sudo cp *.war /var/lib/tomcat7/webapps/

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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-16.23

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).