Introduction

If you simply wish to make use of Saint's annotation capabilities, then you can use a public version of the Saint application. You should also view our user documentation rather than this page. However, if you wish to be able to use the Saint code, and then run your on instance of Saint, then please follow the instructions below.

Prerequisites

Please ensure you have the following correctly installed on your system before attempting to compile and build Saint.

To compile Saint ("mvn compile")

  • Maven 2.x
  • Java 1.5 or higher, with Java 1.6 recommended.
  • libSBML 5.0.0 (Download and Installation). You must make sure that you compile libSBML with the Java libraries. It is fully explained in the linked installation instructions, but essentially you must include the --with-java option when you run ./configure. Once installed, you must manually copy the libsbmlj.jar file from its install location into your local maven 2 repository. Further instructions are in the dependencies section of this project's pom.xml.
  • CellML API 1.9. The best way to get the CellML API is via its pre-compiled, ready-to-use SDK. Information on getting started with the CellML API is also available. Once installed, you must manually copy the cellml.jar file from its install location into your local maven 2 repository. Further instructions are in the dependencies section of this project's pom.xml.

To successfully build the web application ("mvn install")

  • Apache 2
    • or equivalent for your deployment machine.
  • Apache Tomcat
    • or similar for your deployment machine. Whatever system you use, it must be able to accept war files.

Environment Setup

According to the libSBML and CellML installation instructions, you must have the proper java classpath settings and the proper LD_LIBRARY_PATH settings. Please note that these settings are required for Saint to be able to find all of the files required by these libraries (both of these libraries are written in C++ and then java libraries are automatically built on top). Not only do you need to set these in your own build environment, but they also must be set in this project's pom.xml, within the "maven-surefire-plugin" element. Default values are in place there, but you must ensure that these match your environment.

Similarly, on whichever machine you set up tomcat on, you must make these environment variables available to tomcat itself.

Compilation and Installation

  • Go into the saint/trunk directory and run "mvn compile"
  • When that succeeds, you can move on to creating the war file. Run "mvn install".
  • The Saint war file will be in target/saint.war upon successful completion of the install command.