README

Introduction 
============

NuPoP is a software tool for Nucleosome Positioning Prediction. 
For more information on NuPoP and the methods - http://nucleosome.stats.northwestern.edu/


What it does
============

    [a] It can handle multiple fasta sequence in a query file to predict nucleosome occupancy.

    [b] Multiple result file format, Plain text based result and Wiggle fixedStep format based on users request. 
    
    [c] Produce binary files of nucleosome occupency score and corresponding positions in the genomic sequence. 
        The binary file path can be found in NuPoP Log file.


Deployment
==========

    [a] Clone this repository to your local deployment station. 

    [b] Execute the perl script "changePath.pl" to set up the absolute profile file path based on your local station. 
        "perl changePath.pl"

    [c] Please make sure that Biopython is installed in your local station.  

    [d] Move the sample files from test-data folder to galaxy test-data folder.


Contents
========

    src 
    
    [a] Fortran core program. 

    galaxy 

    [a] Pythonic interface to the core program.

    [b] Tool configuration file.

    test-data 

    [a] Test files for running functional tests. 


Contact
=======
    
    Please let me know if you find any difficulty to integrate into Galaxy. I can be reached at vipin <at> cbio.mskcc.org