Mercurial > repos > vipints > deseq_hts

------------------------------------------------------
DESeq2-hts: A Galaxy wrapper for DESeq2 version 1.0.19
------------------------------------------------------

Description:
------------
    DESeq2 can be used as a web service embedded in a Galaxy instance.
    We call it as DESeq2-hts.

Requirements:
-------------
    MATLAB/OCTAVE and Python :- Preprocessing of sequencing reads and GFF files
    R, Bio-conductor package :- Required for DESeq2
    SCIPY, NUMPY :- for python
    SAMTOOLS :- Sequencing read processing

Contents:
---------
    ./src
    All relevant scripts for DESeq-hts are located in the subdirectory
    src. src/deseq2-hts.sh is the main script to start DESeq2-hts. The
    preprocessing of BAM and GFF file start before the R DESeq2 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.sh
    Setup script for DESeq2-hts.

    ./mex
    matlab executable files.

    ./bin
    Contains deseq2_config.sh file which is used for the configuration of
    DESeq2-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.sh and setup paths and configuration options for DESeq2-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 **DESeq2** is used to obtain results for scientific publications it should be cited as [1].

    This wrapper program (DESeq2-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`.

Contact:
--------
    vipin [at] cbio.mskcc.org
author	vipints <vipin@cbio.mskcc.org>
date	Tue, 08 Oct 2013 08:22:45 -0400
parents	2fe512c7bfdf
children