TODO list 
    
    get rid of support for octave from counting  

    compute_sequence_read.py program should work with GTF/GFF file and multiple BAM files
    python to talk with c++ counting script will be a good idea,

    give rights to access count table from other programs too the interface. gff/bam or count table and the condition details

    single dependency folder for tools 

    test-data set more comprehensive 

    






----------------------------------------------------
DESeq-hts: A Galaxy wrapper for DESeq version 1.10.1
----------------------------------------------------

Description:
------------
    DESeq can be used as a web service embedded in a Galaxy instance. 
    We call it as DESeq-hts. 

Requirements:
-------------
    MATLAB/OCTAVE and Python :- Preprocessing of sequencing reads and GFF files
    R, Bio-conductor package :- Required for DESeq 
    SCIPY, NUMPY :- for python  
    SAMTOOLS :- Sequencing read processing 

Contents:
---------
    ./src
    All relevant scripts for DESeq-hts are located in the subdirectory
    src. src/deseq-hts.sh is the main script to start DESeq-hts. The 
    preprocessing of BAM and GFF file start before the R DESeq script. 
	Please follow the shell script to understand the details. 
    
    ./galaxy
    Galaxy tool configuration file can be found galaxy folder. Please 
    make necessary editing for .xml file and remaining .sh files and 
    perform few tests. 

    ./setup_deseq-hts.sh
    Setup script for DESeq-hts.

    ./mex
    matlab executable files.

    ./bin
    Contains deseq_config.sh file which is used for the configuration of 
    DESeq-hts. According to your platform, the default file will be changed.

    ./test_data
    This sub-directory contains all data for running a functional test in
    Galaxy framework. You may need to move these test files into the test-data
    directory.

    ./tools
    A python based GFF parsing program. Also contains small utils programs.

Getting started:
----------------
    Check for all requirements first, then

    a) Run ./setup_deseq-hts.sh and setup paths and configuration options for DESeq-hts.

    b) Inside the mex folder execute the make file to create platform dependent .mex files 
	    cd mex/Makefile 
	    make [interpreter] 
            make octave for octave 
            make matlab for matlab 
            make all for octave and matlab 

    c) Edit the Galaxy tool configuration file to adjust the path if necessary. 

Licenses:
---------
    If **DESeq** is used to obtain results for scientific publications it should be cited as [1].

    This wrapper program (DESeq-hts) is free software; you can redistribute it and/or modify it 
    under the terms of the GNU General Public License as published by the Free Software Foundation; 
    either version 3 of the License, or (at your option) any later version.

    Written (W) 2009-2012 Jonas Behr, Regina Bohnert, Andre Kahles, Gunnar Raetsch, Vipin T. Sreedharan
    Copyright (C) 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany and 
                  2013 cBio Memorial Sloan Kettering Cancer Center, New York City, USA.

References:
-----------
    [1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`. 

Contributions:
--------------
    15 Aug. 2013 
    Philippe Moncuquet
    Bioinformatics Analyst, Bioinformatics Core, CSIRO Mathematics, Informatics and Statistics
    
    Extended the DESeq result.

Contact:
--------
    vipin [at] cbio.mskcc.org