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1 weeder2: motif discovery in sequences from coregulated genes of a single species
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2 ================================================================================
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3
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4 Galaxy tool for the Weeder2 motif discovery package:
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5
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6 - Zambelli, F., Pesole, G. and Pavesi, G. 2014. Using Weeder, Pscan, and PscanChIP
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7 for the Discovery of Enriched Transcription Factor Binding Site Motifs in
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8 Nucleotide Sequences. Current Protocols in Bioinformatics. 47:2.11:2.11.1–2.11.31.
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9 http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0211s47/full
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10
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11 See http://159.149.160.51/modtools/
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12
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13 Automated installation
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14 ======================
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15
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16 Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
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17 the Weeder2 program and data, and setting the appropriate environment variables.
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18
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19 Manual Installation
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20 ===================
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21
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22 There are two files to install:
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23
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24 - ``weeder2_wrapper.xml`` (the Galaxy tool definition)
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25 - ``weeder2_wrapper.sh`` (the shell script wrapper)
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26
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27 The suggested location is in a ``tools/weeder2/`` folder. You will then
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28 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
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29 by adding the line:
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30
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31 <tool file="weeder2/weeder2_wrapper.xml" />
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32
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33 You also need to make a copy of the ``weeder2.loc`` file (a sample version is
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34 provided here) which lists the species for which frequency files are available.
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35 This file should be placed in the ``tool-data`` directory of your Galaxy
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36 installation.
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37
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38 Additionally you will need to install ``weeder2`` from:
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39
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40 - http://159.149.160.51/modtools/downloads/weeder2.html
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41
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42 The tool wrapper uses the following environment variables in order to find the
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43 appropriate files:
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44
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45 - ``WEEDER_FREQFILES_DIR`` should point to the ``FreqFiles`` directory
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46
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47 Also the directory holding the Weeder2 executables should be on your ``PATH``.
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48
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49 Functional tests
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50 ================
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51
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52 If you want to run the functional tests, copy the sample test files under
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53 sample test files under Galaxy's ``test-data/`` directory. Then:
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54
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55 ./run_tests.sh -id weeder2
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56
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57 You will need to have set the environment variables above.
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58
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59 Reference Data
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60 ==============
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61
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62 Weeder2 requires reference data in the form of frequency files for each
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63 species of interest. A set of reference files is provided as part of the
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64 Weeder2 installation.
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65
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66 Additional frequency files can be generated for novel species using the
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67 ``w2frequency_maker`` utility available via:
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68
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69 - http://159.149.160.51/weederaddons/weeder2freq.html
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70
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71 This page also explains what input data should be used.
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72
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73 The location of the additional frequency files can then be specified by
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74 adding them to the ``weeder2.loc`` file (see above).
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75
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76 History
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77 =======
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78
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79 ========== ======================================================================
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80 Version Changes
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81 ---------- ----------------------------------------------------------------------
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82 2.0.3 - Update handling of frequency files to accommodate changes in
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83 latest bioconda version of weeder2.
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84 2.0.2 - Drop ``tool_dependencies.xml`` & use conda to resolve dependencies
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85 2.0.1 - Explicitly specify frequency files in ``weeder2.loc``.
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86 2.0.0 - Initial version
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87 ========== ======================================================================
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88
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89
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90 Developers
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91 ==========
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92
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93 This tool is developed on the following GitHub repository:
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94 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/weeder2
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95
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96 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
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97 the ``package_weeder2.sh`` script.
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98
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99
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100 Licence (MIT)
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101 =============
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102
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103 Permission is hereby granted, free of charge, to any person obtaining a copy
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104 of this software and associated documentation files (the "Software"), to deal
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105 in the Software without restriction, including without limitation the rights
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106 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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107 copies of the Software, and to permit persons to whom the Software is
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108 furnished to do so, subject to the following conditions:
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109
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110 The above copyright notice and this permission notice shall be included in
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111 all copies or substantial portions of the Software.
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112
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113 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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114 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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115 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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116 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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117 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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118 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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119 THE SOFTWARE.
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