USING Clench2:
************
Open a command prompt and navigate to the directory where you 
have Clench2.pl and type Clench2.pl. A usage message:
-----------------------------------------------------------------
Usage:
No arguments provided
Please provide: Organism, BkgIdFile, ClusterFile, ExpFile
-----------------------------------------------------------------
will be displayed.

Then run Clench2.pl with provided sample files.

USE:
****
To run Clench you need to provide the above arguments as follows:

Clench2.pl Organism YourOrganism BkgIdFile YourBkgIdFile ClusterFile YourClusterFile ExpFile YourExpFile

If you have spaces in your file names then double quote filepath and 
name (or better drag-n-drop the files..the quotes will be put automatically).

Organism -	
	Provide name of the organism. You must have a .conf file for
	each organism in the same directory as Clench2.pl. The conf 
	file must be name Clench_OrganismName.conf. See Sample_input_Files
	for an example (Clench_Arabidopsis.conf).
				
BkgIdFile -
	Provide full path and name of the file containing
	  a list of genes (one per line) that serve as 'reference'.
	  See Sample_input_Files for an example (BkgIdFile.txt)

ClusterFile -
	Provide full path and name of the file containing
	  a list of genes (one per line) that belong to a cluster.
	  See Sample_input_Files for an example (ClusterFile.txt)
	OR
	A file containing a list of Clusterfiles.
	See Sample_input_Files for an example (ClusterFileList.txt)
				
ExpFile -
	Provide full path and name of the file containing the 
	microarray expression data as a tab delimited text file.
	See Sample_input_Files for an example (ExpFile.txt)
						
IMP: ** See Clench_OrganismName.conf for other required parameters to provide.**
IMP: ** See SampleFiles_for_conf for other required files to provide.**