RIPE: Regulatory Network Inference Files

Preliminaries
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The ripe package is dependent on a Matlab executable file and a MATLAB Compiler Runtime (MCR), a standalone set of shared libraries that enable the execution of M-files.

Download the ripe package (current version ripe_1.1.tar.gz) and the MCR matching your architecture.

The ripe package is dependent on the following R packages: SparseM, glmnet, igraph, and graph. Make sure you have them installed before you continue. The first three packages are available on CRAN (http://cran.r-project.org/) while the graph package can be fetched from Bioconductor (http://www.bioconductor.org/). 

Compiling from source on Windows
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o. Install Rtools if needed.

	Make sure you have Rtools installed, which is needed to compile the ripe package. Rtools is available on CRAN via http://cran.r-project.org/bin/windows/Rtools/. While installing Rtools, make sure to select the option to edit the PATH to include Rtools on it.

o. Run the MCR installer. 

       The installer usually adds the MCR to the PATH variable. 

	You can check this via (Control panel -> System and Security -> System -> Advanced system settings -> Environment Variables). If not on the path, for Win32 add <mcr_root>\v713\runtime\win32, where <mcr_root is where you chose to install the MCR. For Win64 add <mcr_root>\v715\runtime\win64. The path that is needed should point to a set of dll files. 

o. Install the R package. From within R, type

	install.packages("ripe_1.1.tar.gz", repos=NULL,type="source", INSTALL_opts=c('--force-biarch'))
   
   If you get an error, try instead

	install.packages("ripe_1.1.tar.gz", repos=NULL,type="source")

Make sure you have set the current directory to where you saved the tar.gz file. 


Compile from source on Mac OS X 
======================

o. Run the MCR installer. 

       Install the MCR in a location of your choice, e.g. /Applications/MATLAB/MATLAB_Compiler_Runtime. You will need the path adding the directory v82, e.g. /Applications/MATLAB/MATLAB_Compiler_Runtime/v82 (denoted <m_path>).

o. Install the ripe package in R by

   (a) typing the following from the command line:
       R CMD INSTALL --configure-args='--with-mpath=<m_path>' ripe_1.1.tar.gz

       or

   (b) install.packages("ripe_1.1.tar.gz",repos=NULL,type='source',configure.args='--with-mpath=<m_path>')


Either way, you have to give the path to the MCR to the R CMD INSTALL function.