INSTALL

Installation instructions:

1. Check installation for the existence of ./ASP/clingo
If it’s not there download the new clingo (http://sourceforge.net/projects/potassco/files/clingo) from the website and rename it to that file.
 
You can try running:
	./ASP/clingo
to see whether your clingo installation is working.


2. Install R packages:

source('http://bioconductor.org/biocLite.R')
biocLite(c('graph','RBGL','gmp','RcppArmadillo'))
install.packages(c('deal','pcalg','combinat','hash','bnlearn','foreach','doMC','caTools','expm'))


3. Start R in the "R/" directory and load the code with the following commands:
> source('load.R')
> loud() 
Optionally you can specify how many cores you would like to run in parallel with (e.g. 4) with:
> loud(4) 


4. Test the installation by running an experiment: a simulated graph with 4 nodes
> pipeline()

You can now run other experiments using the pipeline() function.

If you want to run it on non-simulated data, you can pass a table of experimental data in the parameter ‘samples’ to pipeline().

In order to use the parallel resolution, you also need to specify ‘multipleMinima=“iterativeParallel'
There are several other options for pipeline(), described in its documentation at pipeline.R.