Overview

Installation
============
To install MetaNetSam, please follow the steps below:

1. Install Java6 or above. 
2. Download the binary jar file. 

Running the program
===================
To run MetaNetSam, using the reference metabolic network built from KEGG reaction database, 

java -cp metanetsam-<version>.jar metanetsam.KeggNetwork
 -b,--burn-in <arg>         num. of burn-in samples (optional, default: 10000000)
 -f,--genome-filter <arg>   Class name of GenomeFilter (optional, default: metanetsam.io.filter.FirstColumnKOFileFilter)
 -g,--genome-file <arg>     File that used by Genome Filter (required)
 -i,--iterations <arg>      num of iterations (optional, default: 210000000)
 -o,--output <arg>          output directory (required)
 -s,--batch-size <arg>      batch sampling size (optional, default: 10000)
 -v,--verbose               write more chain data (optional)
 
--genome-file is a tab-delimited text file in which each line represents a KEGG ortholog, and the first column 
in the file is the KO number. Data in the rest of the line are not used so can be artitrary or the file can 
has only one column.