ConsensusCluster PCA and Clustering Utility

Copyright Michael Seiler 2008

Rutgers University
miseiler@gmail.com

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Contents:

	1. Installation

	2. Running

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1. INSTALLATION

	A. Dependencies

		This program requires the following packages to be correctly installed:

		Python				>= 2.5
		Python-numpy		>= 1.1.0

		In addition, the following optional packages greatly enhance capability:	
	
		Python-matplotlib	>= 0.98.0	(For plots)
		Python-pil			>= 1.1.6	(For consensus matrix heatmaps)
		Python-pygtk					(GUI)
		Python-scipy					(For ttest only, more in the future)
	
		psyco		(JIT compiler, speed)
		GCC			(Compiler, see Optionally Compile C Extensions below)
		GNU Make	(see Optionally Compile C Extensions below)
		pyMPI		(MPI-compatibility, enables multiprocessor support)

		Optional dependencies are not required and the program will function without them.

		This program *MAY* work with versions earlier than those listed, but this has not been tested
		and such use is unsupported.

	B. Installation

		To install, simply untar the package into a new directory.

	C. Optionally Compile C Extensions (Linux)

		Optionally, one can compile the external C modules, which are located in the euclidean and SA directories.
		To compile these, change to the directory, and run make.

		Example:

			cd euclidean
			make && make install

		Compilation requires python development files, numpy development files, GCC, and GNU make.

		These extensions are not required, however the program is much slower without them.

	D. Install precompiled 32-bit C Extensions (Windows)

		Run the installers in the euclidean and SA directories.
		
		These extensions are not required, however the program is much slower without them.

2. RUNNING

	A. Running ConsensusCluster (Single Processor, Linux and Windows)

		To run the program, simply type the following from the installation directory:
	
			python common.py
	
		Or run common.py from any file manager.

		This will bring up the GUI if pygtk is correctly installed. If not, please see 'python common.py --help'
		for a complete list of command line options.

	B. Running ConsensusCluster (MultiProcessor, Linux)

		If pyMPI is installed and MPI is setup correctly, the following command enables multiprocessor support:
	
			mpirun -np 2 pyMPI migration.py
	
		Replace "mpirun -np 2" with the appropriate MPI command as required by your MPI installation.