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1 ---------------------------------------------------
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2 DESeq-hts: A Galaxy wrapper for DESeq version 1.6.0
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3 ---------------------------------------------------
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4
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5 Description:
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6 DESeq can be used as a web service embedded in a Galaxy instance.
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7 We call it as DESeq-hts.
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8
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9 Requirements:
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10 MATLAB/OCTAVE and Python :- Preprocessing of sequencing reads and GFF files
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11 R, Bio-conductor package :- Required for DESEQ
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12 SCIPY, NUMPY :- for python
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13 SAMTOOLS :- Read processing
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14
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15 Contents:
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16 [src]
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17 All relevant scripts for DESeq-hts are located in the subdirectory
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18 src. src/deseq.sh is the main script to start DESeq-hts. The
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19 preprocessing of BAM and GFF file start before the R DESEQ script.
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20 Please follow the shell script to understand the details.
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21
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22 [galaxy]
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23 Galaxy tool configuration file can be found galaxy folder. Please
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24 make necessary editing for .xml file and remaining .sh files and
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25 perform few tests.
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26
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27 [setup_deseq-hts.sh]
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28 Setup script for DESeq-hts.
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29
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30 [mex]
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31 matlab executable files.
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32
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33 [bin]
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34 Contains deseq_config.sh file which is used for the configuration of
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35 DESeq-hts. According to your platform, the default file will be changed.
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36
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37 [test_data]
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38 This subsirectory contains all data for running a functional test in
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39 Galaxy framework. You may need to move these test files into the test-data
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40 directory.
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41
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42 [tools]
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43 A python based GFF parsing program. Also contains small utils programs.
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44
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45 Getting started:
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46 Check for all requirements first, then
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47
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48 a) Run ./setup_deseq-hts.sh and setup paths and configuration options for DESeq-hts.
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49
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50 b) Inside the mex folder execute the make file to create platform dependent .mex files
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51 cd mex/Makefile
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52 make [interpreter]
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53 make octave for octave
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54 make matlab for matlab
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55 make all for octave and matlab
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56
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57 c) Edit the Galaxy tool configuration file to adjust the path if necessary.
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58
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59 Licenses:
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60 If **DESeq** is used to obtain results for scientific publications it should be cited as [1].
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61
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62 This wrapper program (DESeq-hts) is free software; you can redistribute it and/or modify it
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63 under the terms of the GNU General Public License as published by the Free Software Foundation;
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64 either version 3 of the License, or (at your option) any later version.
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65
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66 Written (W) 2009-2012 Jonas Behr, Regina Bohnert, Andre Kahles, Gunnar Raetsch, Vipin T. Sreedharan
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67 Copyright (C) 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany and
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68 2012 cBio Memorial Sloan Kettering Cancer Center, New York City, USA.
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69
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70 References:
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71 [1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`.
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72
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73 Contact:
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74 vipin@cbio.mskcc.org
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75
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