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.
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Overview
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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-16.2.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
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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 |
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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. |
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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
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cd ~
echo "export PATH=${HOME}/transmart/transmart-data/R/root/bin:$PATH" > Rpath.sh
sudo mv Rpath.sh /etc/profile.d/ |
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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:
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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-16.2
FAQs
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Start with the Sanity Checklist. If that is successful, you can work through the exercises provided in the user guide. |
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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:
Developers/Administrators:
You can use a band of IPs if you are unable to get an exact IP address. |
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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).
