weka-GWAVA

Weka implementation of the GWAVA method from Ritchie, G. R. S., Dunham, I., Zeggini, E., & Flicek, P. (2014). Functional annotation of noncoding sequence variants. Nat Methods, 11(3), 294–296. http://doi.org/10.1038/nmeth.2832

Requirements

weka-GWAVA requires java 8 and higher. It can be used as a Weka plugin using version 3.9 or higher. To build the program it is recommended to use Maven.

Installation from GitHub sources

To use weka-GWAVA in Weka three steps are needed.

1. Clone this repository.
2. Compile the java classes and create a Weka plugin using Maven
3. Load the plugin into your Weka Package Manager

Clone this repository

Use your terminal and go to a folder where you want to checkout weka-GWAVA. Then run:

git clone https://github.com/charite/weka-GWAVA.git

Compile the java classes and create the Weka plugin

Go to your repository and create a jar file of weka-GWAVA using Maven.

cd weka-GWAVA

mvn clean install package

Now you should have the weka-GWAVA-0.1.jar in the folder target/. The package phase of Maven creates also the Weka file weka-GWAVA-0.1-weka.zip. It is located in the target/ folder.

Load the plugin into your Weka Package Manager

Open Weka, go to the package manager, and load the file weka-GWAVA-0.2-weka.zip into it. Look at the Weka wiki for more information about the Weka Package Manager.