ESSNet is a program that was developed by Dr. Lim et al. at the University of Singapore for studying relationships between entities in biological pathways.

1. Install Homebrew if you don't have it installed already. The instructions on their website should suffice.

2. The first package we will install is R. In order to gain access to the R installer under homebrew, you need to add the following repository.

   brew tap homebrew/science

3. Once the repository is added run the following command. The prompts during the installation will guide you through the necessary steps.

   brew install r

4. Once you have R installed, type r then enter to initiate the r shell. If the installation went successfully, you should be greeted by the r shell.

5. Next we need to install the R dependencies that ESSNet relies on and are avaliable on the R distribution network. In the prompt, type the following commands.

   install.packages("rJava")
   install.packages("igraph")
   

   You may be prompted to selected a CRAN mirror. If so, select a mirror that is closest to your geographical location for the fastest download times.

6. After the packages are installed, type q() to exit the r shell.

7. Next, install Apache ant

   brew install ant

8. Finally, make sure that you have JDK 7 installed.

9. ESSNet relies on another package called PFSnet which we need to install before we install ESSnet. Change directory to a writeable folder such as ~/Downloads and run the following in terminal:

   curl -o pfsnet.tar.gz 'http://compbio.ddns.comp.nus.edu.sg/~intpath/ftp/Storage/pfsnet_1.0.tar.gz'
   tar xvzf pfsnet.tar.gz
   r CMD install pfsnet

   If successful, you will receive output similar to this:

   asaji@asaji:~/Downloads$ r CMD install pfsnet
   installing to library ‘/usr/local/Cellar/r/3.1.0/R.framework/Versions/3.1/Resources/library’
   installing source package ‘pfsnet’ ...
   libs
   ant clean
   Buildfile: /Users/asaji/Downloads/pfsnet/src/build.xml
   
   clean:
   BUILD SUCCESSFUL
   Total time: 0 seconds
   R
   inst
   preparing package for lazy loading
   help
   installing help indices
   building package indices
   testing if installed package can be loaded
   DONE (pfsnet)

10. Now we can download and install ESSNet. Once again, make sure you are in a writeable directory and run the following commands in terminal:

    curl -o essnet.tar.gz 'http://compbio.ddns.comp.nus.edu.sg:8080/essnet/downloads/essnet_1.0.tar.gz'
    tar xvzf essnet.tar.gz
    r CMD install essnet

    If successful, you will receive output similar to this:

    asaji@asaji:~/Downloads$ r CMD install essnet
    * installing to library ‘/usr/local/Cellar/r/3.1.0/R.framework/Versions/3.1/Resources/library’
    * installing source package ‘essnet’ ...
    ** libs
    ant clean
    Buildfile: /Users/asaji/Downloads/essnet/src/build.xml
    
    clean:
    BUILD SUCCESSFUL
    Total time: 0 seconds
    R
    inst
    preparing package for lazy loading
    help
    Warning: /Users/asaji/Downloads/essnet/man/essnet-package.Rd:33: All text must be in a section
    Warning: /Users/asaji/Downloads/essnet/man/essnet-package.Rd:34: All text must be in a section
    installing help indices
    building package indices
    testing if installed package can be loaded
    DONE (essnet)

11. You should now be able to successfully run ESSnet in R.