Installation

Downloading with EpiFusionUtilities

If you wish to exclusively use EpiFusion within R, it is possible to do so through the EpiFusionUtilities R package, which comes with the latest stable version of EpiFusion and is callable from R with the function run_epifusion(). EpiFusionUtilities is installable using devtools with the R command:

devtools::install_github("https://github.com/ciarajudge/EpiFusionUtilities")

Manually downloading the executable file

To install EpiFusion, go to the releases page of the Github repository and download the latest executable (jar) file. It really is that simple - you can start using the program straight away by running the file with Java. Consider carefully which directory you place the file in, as every time you wish to use EpiFusion you'll have to call it with its file path. You can also call EpiFusion from any working directory on your system by creating a symbolic link.

Creating a symbolic link

As above, download an EpiFusion jar file and place it wherever you'd like on your system. Somewhere like /usr/local/bin could do the trick. Open a terminal window and type

echo $PATH

Navigate to one of the filepaths that appears, again it will probably be something like /usr/local/bin. Then you want to make a bash script that will run EpiFusion and pass whatever arguments to it. You can do this with a text editor like 'nano' or 'vim'. The bash script can be called anything, but it should contain the following content:

#!/bin/bash
java -jar /absolute/path/to/EpiFusion/jar/file.jar "$@"

Then you want to create a symbolic link between this script and the keyword 'EpiFusion'. You can do that by typing the following command:

ln -s /path/to/wherever/the/bash/script/was/made EpiFusion

Now you should be able to call EpiFusion from anywhere in your system.