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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 For example, using https://doi.org/10.5281/zenodo.1406071 which is the
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49 database provided with Kodoja::
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50
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51 $ cd /mnt/shared/data/
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52 $ mkdir kodojaDB_v1.0
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53 $ cd kodojaDB_v1.0
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54 $ wget https://zenodo.org/record/1406071/files/kodojaDB_v1.0.tar.gz
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55 $ tar -zxvf kodojaDB_v1.0.tar.gz
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56
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57 Each installed version of Kodoja (or Kraken or Kaiju) will have its own
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58 ``*.loc`` files, which Galaxy will merge into a single list. e.g.::
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59
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60 $ find /path/to/galaxy/tool-data -name kaiju_databases.loc
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61 $ find /path/to/galaxy/tool-data -name kraken_databases.loc
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62
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63 Edit a ``kraken_databases.loc`` file to add a line like this, where
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64 ``(tab)`` represents inserting a tab character (NOT spaces)::
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65
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66 kodojaDB_v1.0_kraken(tab)KodojaDB v1.0 (kraken), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/krakenDB
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67
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68 And likewise update ``kaiju_databases.loc`` with a line like::
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69
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70 kodojaDB_v1.0_kaiju(tab)KodojaDB v1.0 (kaiju), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/kaijuDB
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71
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72 At the time of writing, reloading the ``*.loc`` files required restarting
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73 the Galaxy server, or doing this explicitly via the "Data tables registry"
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74 available under Server Administration if logged into Galaxy as an administator.
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75
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76 It is our personal preference to work with ``tool-data/kraken_databases.loc``
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77 and ``tool-data/kaiju_databases.loc``, but if these are being ignored, you
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78 *may* need to enable this by adding the XML data table entries from our file
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79 ``tool_data_table_conf.xml.sample`` to ``config/tool_data_table_conf.xml``.
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1
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80
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81
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82 History
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83 =======
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84
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85 ======= ======================================================================
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86 Version Changes
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87 ------- ----------------------------------------------------------------------
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88 v0.0.0 - Initial release covering ``kodoja_search.py`` v0.0.3.
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89 v0.0.4 - Minor update to call ``kodoja_search.py`` v0.0.4.
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90 v0.0.6 - Minor update to call ``kodoja_search.py`` v0.0.6.
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91 - Document installing the Kodoja databases from Zenodo.
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92 v0.0.7 - Minor update to call ``kodoja_search.py`` v0.0.6.
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93 - Update help text, including zeros in columns 6 and 7.
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94 - Support ``$GALAXY_SLOTS``, defaulting to using four threads.
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95 v0.0.8 - Minor update to call ``kodoja_search.py`` v0.0.8.
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96 - Option to capture the ``kodoja_VRL.tsv`` read table.
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97 - Accept ``kraken_databases.loc`` entry style for old Kraken wrapper.
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98 ======= ======================================================================
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99
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100
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101 Bug Reports
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102 ===========
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103
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104 File a Galaxy wrapper issue at https://github.com/abaizan/kodoja_galaxy/issues
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105
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106 For issues with Kodoja itself, use https://github.com/abaizan/kodoja/issues
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107
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108
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109 Developers
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110 ==========
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111
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112 For pushing a release to the test or main "Galaxy Tool Shed", use the
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113 following Planemo commands (which requires you have set your Tool Shed access
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114 details in ``~/.planemo.yml`` and that you have access rights on the Tool
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115 Shed)::
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116
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117 $ planemo shed_update -t testtoolshed --check_diff .
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118 ...
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119
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120 or::
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121
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122 $ planemo shed_update -t toolshed --check_diff .
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123 ...
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124
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125 To just build and check the tar ball, use::
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126
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127 $ planemo shed_upload -t testtoolshed --tar_only .
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128 ...
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129 $ tar -tzf shed_upload.tar.gz
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130 LICENSE
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131 README.rst
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132 ...
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133
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134 This simplifies ensuring a consistent set of files is bundled each time,
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135 including all the relevant test files.
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136
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137
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138 Licence (MIT)
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139 =============
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140
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141 Permission is hereby granted, free of charge, to any person obtaining a copy
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142 of this software and associated documentation files (the "Software"), to deal
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143 in the Software without restriction, including without limitation the rights
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144 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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145 copies of the Software, and to permit persons to whom the Software is
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146 furnished to do so, subject to the following conditions:
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147
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148 The above copyright notice and this permission notice shall be included in
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149 all copies or substantial portions of the Software.
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150
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151 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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152 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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153 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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154 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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155 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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156 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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157 THE SOFTWARE.
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