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1 .. image:: https://travis-ci.org/abaizan/kodoja_galaxy.svg?branch=master
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2 :alt: Linux testing with TravisCI
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3 :target: https://travis-ci.org/abaizan/kodoja_galaxy/branches
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4
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5 This is a Galaxy wrapper for the tool Kodoja, which is available to install in
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6 conda from bioconda.
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7
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8 https://github.com/abaizan/kodoja
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9
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10 Galaxy wrappers for Kodoja
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11 ==========================
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12
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13 These wrappers are copyright 2018 by Amanda Baizan Edge (University of
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14 St Andrews, and The James Hutton Institute) and Peter Cock (The James
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15 Hutton Institute). They are released under the MIT licence.
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16
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17 These wrappers are available from the Galaxy Tool Shed at:
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18 http://toolshed.g2.bx.psu.edu/view/abaizan/kodoja
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19
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20 In-development test releases are available from the Test Tool Shed at:
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21 http://testtoolshed.g2.bx.psu.edu/view/abaizan/kodoja
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22
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23
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24 Citation
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25 ========
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26
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27 Please refer to the main Kodoja citation instructions.
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28
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29
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30 Automated Installation
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31 ======================
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32
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33 Galaxy should be able to automatically install the dependencies, namely
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34 ``kodoja`` and its dependencies like ``kraken`` and ``kaiju``, using the
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35 conda and the bioconda recipes.
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36
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37 See the configuration notes below.
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38
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39
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40 Configuration
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41 =============
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42
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43 You must tell Galaxy about any Kraken and Kaiju databases using configuration
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44 files ``kraken_databases.loc`` and ``kaiju_databases.loc`` which are located
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45 in the ``tool-data/`` folder. Sample files are included which explain the
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46 tab-based format to use.
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47
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48
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49 History
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50 =======
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51
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52 ======= ======================================================================
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53 Version Changes
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54 ------- ----------------------------------------------------------------------
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55 v0.0.0 - Initial release covering ``kodoja_search.py`` v0.0.3.
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56 ======= ======================================================================
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57
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58
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59 Bug Reports
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60 ===========
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61
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62 File a Galaxy wrapper issue at https://github.com/abaizan/kodoja_galaxy/issues
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63
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64 For issues with Kodoja itself, use https://github.com/abaizan/kodoja/issues
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65
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66
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67 Developers
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68 ==========
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69
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70 For pushing a release to the test or main "Galaxy Tool Shed", use the
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71 following Planemo commands (which requires you have set your Tool Shed access
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72 details in ``~/.planemo.yml`` and that you have access rights on the Tool
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73 Shed)::
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74
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75 $ planemo shed_update -t testtoolshed --check_diff .
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76 ...
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77
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78 or::
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79
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80 $ planemo shed_update -t toolshed --check_diff .
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81 ...
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82
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83 To just build and check the tar ball, use::
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84
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85 $ planemo shed_upload -t testtoolshed --tar_only .
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86 ...
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87 $ tar -tzf shed_upload.tar.gz
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88 LICENSE
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89 README.rst
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90 ...
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91
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92 This simplifies ensuring a consistent set of files is bundled each time,
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93 including all the relevant test files.
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94
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95
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96 Licence (MIT)
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97 =============
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98
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99 Permission is hereby granted, free of charge, to any person obtaining a copy
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100 of this software and associated documentation files (the "Software"), to deal
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101 in the Software without restriction, including without limitation the rights
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102 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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103 copies of the Software, and to permit persons to whom the Software is
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104 furnished to do so, subject to the following conditions:
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105
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106 The above copyright notice and this permission notice shall be included in
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107 all copies or substantial portions of the Software.
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108
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109 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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110 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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111 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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112 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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113 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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114 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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115 THE SOFTWARE.
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