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1 ----------------------------------------------------
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2 DESeq: A Galaxy wrapper for DESeq version 1.12.1
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3 ----------------------------------------------------
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4
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5 Description:
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6 ------------
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7 DESeq can be used as a web service embedded in a Galaxy instance.
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8 We call it as DESeq-hts.
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10 Requirements:
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11 -------------
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12 MATLAB/OCTAVE and Python :- Preprocessing of sequencing reads and GFF files
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13 R, Bio-conductor package :- Required for DESeq
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14 SCIPY, NUMPY :- for python
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15 SAMTOOLS :- Sequencing read processing
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16
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17 Contents:
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18 ---------
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19 ./src
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20 All relevant scripts for DESeq-hts are located in the subdirectory
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21 src. src/deseq-hts.sh is the main script to start DESeq-hts. The
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22 preprocessing of BAM and GFF file start before the R DESeq script.
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23 Please follow the shell script to understand the details.
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24
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25 ./galaxy
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26 Galaxy tool configuration file can be found galaxy folder. Please
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27 make necessary editing for .xml file and remaining .sh files and
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28 perform few tests.
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29
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30 ./setup_deseq-hts.sh
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31 Setup script for DESeq-hts.
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32
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33 ./mex
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34 matlab executable files.
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35
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36 ./bin
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37 Contains deseq_config.sh file which is used for the configuration of
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38 DESeq-hts. According to your platform, the default file will be changed.
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39
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40 ./test_data
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41 This sub-directory contains all data for running a functional test in
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42 Galaxy framework. You may need to move these test files into the test-data
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43 directory.
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44
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45 ./tools
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46 A python based GFF parsing program. Also contains small utils programs.
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47
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48 Getting started:
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49 ----------------
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50 Check for all requirements first, then
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51
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52 a) Run ./setup_deseq-hts.sh and setup paths and configuration options for DESeq-hts.
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53
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54 b) Inside the mex folder execute the make file to create platform dependent .mex files
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55 cd mex/Makefile
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56 make [interpreter]
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57 make octave for octave
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58 make matlab for matlab
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59 make all for octave and matlab
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60
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61 c) Edit the Galaxy tool configuration file to adjust the path if necessary.
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62
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63 Licenses:
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64 ---------
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65 If **DESeq** is used to obtain results for scientific publications it should be cited as [1].
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66
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67 This wrapper program (DESeq-hts) is free software; you can redistribute it and/or modify it
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68 under the terms of the GNU General Public License as published by the Free Software Foundation;
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69 either version 3 of the License, or (at your option) any later version.
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70
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71 Written (W) 2009-2012 Jonas Behr, Regina Bohnert, Andre Kahles, Gunnar Raetsch, Vipin T. Sreedharan
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72 Copyright (C) 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany and
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73 2013 cBio Memorial Sloan Kettering Cancer Center, New York City, USA.
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74
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75 References:
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76 -----------
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77 [1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`.
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78
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79 Contributions:
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80 --------------
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81 15 Aug. 2013
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82 Philippe Moncuquet
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83 Bioinformatics Analyst, Bioinformatics Core, CSIRO Mathematics, Informatics and Statistics
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84
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85 Extended the DESeq result.
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86
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87 Contact:
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88 --------
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89 support [at] oqtans.org
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90
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