Installation

Before installing RAMPART please ensure any dependencies listed above are installed. In addition, the following dependencies are required to install and run RAMPART:

  • Java Runtime Environment (JRE) V1.7+

RAMPART can be installed either from a distributable tarball, or from source via a git clone. These steps are described below. Before that however, here are a few things to keep in mind during the installation process:

From tarball

RAMPART is available as a distributable tarball. The installation process is simply involves unpacking the compressed tarball to a directory of your choice: tar -xvf <name_of_tarball>. This will create a directory called rampart-<version> and in there should be the following sub-directories:

  • bin - contains the main rampart script and other utility scripts
  • doc - a html and pdf copy of this manual
  • etc - contains default environment configuration files, and some example job configuration files
  • man - contains a copy of the manual in man form
  • repo - contains the java classes used to program the pipeline
  • support_jars - contains source and javadocs for the main rampart codebase

Should you want to run the tools without referring to their paths, you should ensure the ‘bin’ sub-directory is on your PATH environment variable.

From source

RAMPART is a java 1.7 / maven project. Before compiling the source code, please make sure the following dependencies are installed:

  • GIT
  • Maven 3
  • JDK v1.7+
  • Sphinx and texlive (If you would like to compile this documentation. If these are not installed you must comment out the create-manual execution element from the pom.xml file.)

You also need to make sure that the system to are compiling on has internet access, as it will try to automatically incorporate any required java dependencies via maven. Now type the following:

git clone https://github.com/TGAC/RAMPART.git
cd RAMPART
mvn clean install

Note: If you cannot clone the git repositories using “https”, please try “ssh” instead. Consult github to obtain the specific URLs.

Assuming there were no compilation errors. The build, hopefully the same as that described in the previous section, can now be found in ./build/rampart-<version>. There should also be a dist sub directory which will contain a tarball suitable for installing RAMPART on other systems.