================================================================================
SigWin/WS-VLAM modules README file. 
================================================================================
Revision: 1.1 March 25, 2008. (Sample templates added.) 
Version: 1.0 February 15, 2008. 
Author:
    Marcia A. Inda
    Integrative Bioinformatics Unit, UvA
    http://staff.science.uva.nl/~inda 
================================================================================
CONTENTS:
1. Introduction
2. Tar file contents
3. Trying SigWin-detector
4. Requirements
5. Installing the modules
6. Sample templates and help
================================================================================

1.Introduction:
    This tar file contains the source files of the WS-VLAM modules needed to run 
the SigWin-detector workflow. 

2.Tar file contents:
    The tar file contains the following files/directories:
    README.txt: This file.
    module_descriptions: The xml files containing the modules definitions. 
    	    Needed for WS-VLAM client distribution.
    mymodules: The source code of the modules. 
    	    Needed for WS-VLAM site distribution.
    docs: The html documentation of the modules. 
    templates: Sample SigWin-detector configurations (templates).
    SampleDate: Sample data.
    SigWin-detector-Workflows.htm: describes how to use the sample templates.

3. Trying SigWin-detector:
    A complete installation of WS-VLAM requires a GLOBUS GT4 installation, and
Grid certificates. If you do not have access to a WS-VLAM site installation 
(e.g., at fs2.das3.science.uva.nl) you may want to try it first. In this case please contact me (inda@science.uva.nl) or someone in the WS-VLAM development
team (gvlam@lists.vl-e.nl).
    In this case you will only need the WS-VLAM client distribution.


4.Requirements:
    To run SigWin-detector you need access to an installation of the WS-VLAM 
workflow management system. WS-VLAM has a client distribution and site distribution. 
    
    i)  WS-VLAM client distribution: The WS-VLAM composer, a graphical 
    	interface used for creating, modifying, and submitting workflows.
	
    ii) WS-VLAM site distribution: The WS-VLAM engine, which is needed for 
    	running the workflows in a Grid. The WS-VLAM engine needs a GLOBUS GT4
	(4.0.3) installation.

To dowload these WS-VLAM distributions go to
http://staff.science.uva.nl/~gvlam/wsvlam/, click the "Distributions" and 
follow the instructions in it. If you have problems please contact someone in
the WS_VLAM development team (gvlam@lists.vl-e.nl).

    
5. Installing the modules:
    After installing WS-VLAM you need to install the modules. 
(First check if they where not included in the WS-VLAM distribution.)
    i)  In the client side:
    	Copy the xml definition files from the directory module_descriptions to
your local modules repository.
    ii) In the site side:
    	- go to the mymodules directory
	cd mymodules
	- compile the modules:
	make
	- copy the executables to the $VLAM_HOME/modules directory
	./copy.sh <VLAM_HOME directory>

6.  Sample templates and help
    This distribution come with 5 sample SigWin-detector templates:
        - SigWin-detector_Confic-Basic.xml
        - SigWin-detector_Config-Basic2.xml
        - SigWin-detector_Config-Sub.xml, or 
        - SigWin-detector_Config-Sub2.xml
        - SigWin-mmFDR-sub.xml (an optimized version of
	  SigWin-detector_Config-Sub.xml)
    An explanation on how to use them can be found in the
    SigWin-detector-Workflows.htm file. 
    
    Manual pages for the modules can be found in SigWin-detector home page. 
    Alternatively you can use doxygen to extract the documentation from the 
    modules source code. 

================================================================================