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annotate tools/effectiveT3/README.rst @ 6:0f6eb4a75000 draft

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v0.0.15 internal changes; v0.0.14 fixed error handling
author peterjc
date Wed, 05 Aug 2015 11:04:42 -0400
parents 1ea715da1879
children 5f85301d50bf
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1 Galaxy wrapper for EffectiveT3 v1.0.1
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2 =====================================
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3
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4 This wrapper is copyright 2011-2015 by Peter Cock, The James Hutton Institute
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5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
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6 See the licence text below.
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7
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8 This is a wrapper for the command line Java tool EffectiveT3, v1.0.1,
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9
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10 Jehl, Arnold and Rattei.
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11 Effective - a database of predicted secreted bacterial proteins
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12 Nucleic Acids Research, 39(Database issue), D591-5, 2011.
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13 http://dx.doi.org/10.1093/nar/gkq1154
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15 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei.
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16 Sequence-based prediction of type III secreted proteins.
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17 PLoS Pathog. 5(4):e1000376, 2009.
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18 http://dx.doi.org/10.1371/journal.ppat.1000376
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19
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20 http://effectors.org/
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22 This wrapper is available from the Galaxy Tool Shed at:
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23 http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
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26 Automated Installation
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27 ======================
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29 This should be straightforward, Galaxy should automatically download and install
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30 the Jar files for effectiveT3 v1.0.1 and the three models (animal, plant and std).
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33 Manual Installation
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34 ===================
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36 You can change the path by setting the environment variable ``$EFFECTIVET3`` to the
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37 relevant folder, but by default it expects the following files to be installed
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38 at these locations::
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40 /opt/EffectiveT3/TTSS_GUI-1.0.1.jar
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41 /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar
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42 /opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar
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43 /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar
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45 To install the wrapper copy or move the following files under the Galaxy tools
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46 folder, e.g. in a tools/effectiveT3 folder:
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47
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48 * ``effectiveT3.xml`` (the Galaxy tool definition)
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49 * ``effectiveT3.py`` (the Python wrapper script)
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50 * ``README.rst`` (this file)
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51
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52 Also copy ``effectiveT3.loc.sample`` to ``effectiveT3.loc`` in the ``tool-data``
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53 folder (and edit if appropriate, e.g. to add or remove a model).
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55 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
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56 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
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57 it next to them. Just add the line::
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59 <tool file="effectiveT3/effectiveT3.xml" />
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61 If you wish to run the unit tests, also move/copy the ``test-data/`` files
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62 under Galaxy's ``test-data/`` folder. Then::
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64 $ ./run_tests.sh -id effectiveT3
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65
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66 That's it.
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69 History
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70 =======
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72 ======= ======================================================================
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73 Version Changes
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74 ------- ----------------------------------------------------------------------
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75 v0.0.7 - Initial public release
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76 v0.0.8 - Include effectiveT3.loc.sample in Tool Shed
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77 v0.0.9 - Check the return code for errors in the XML
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78 v0.0.10 - Added unit test
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79 v0.0.11 - Automated installation
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80 - Record version of Python script when called from Galaxy
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81 - Link to Tool Shed added to help text and this documentation.
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82 v0.0.12 - More explicit naming of the output dataset.
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83 - Adopt standard MIT licence.
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84 - Use reStructuredText for this README file.
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85 - Updated citation information (Cock et al. 2013).
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86 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
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87 v0.0.13 - Relax unit test to allow for small floating point score difference.
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88 - Tool definition now embeds citation information.
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89 v0.0.14 - Fixed error handling in ``effectiveT3.py``.
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90 v0.0.15 - Reorder XML elements (internal change only).
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91 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
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92 ======= ======================================================================
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94
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95 Developers
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96 ==========
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97
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98 This script and related tools were initially developed on the following hg branch:
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99 http://bitbucket.org/peterjc/galaxy-central/src/tools
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100
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101 Development has now moved to a dedicated GitHub repository:
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102 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
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103
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104 For pushing a release to the test or main "Galaxy Tool Shed", use the following
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105 Planemo commands (which requires you have set your Tool Shed access details in
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106 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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107
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108 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/effectiveT3/
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109 ...
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110
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111 or::
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112
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113 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/effectiveT3/
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114 ...
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115
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116 To just build and check the tar ball, use::
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117
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118 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/effectiveT3/
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119 ...
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120 $ tar -tzf shed_upload.tar.gz
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121 tool-data/effectiveT3.loc.sample
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122 test-data/empty.fasta
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123 test-data/empty_effectiveT3.tabular
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124 test-data/four_human_proteins.fasta
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125 test-data/four_human_proteins.effectiveT3.tabular
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126 tool-data/effectiveT3.loc.sample
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127 tools/effectiveT3/README.rst
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128 tools/effectiveT3/effectiveT3.py
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129 tools/effectiveT3/effectiveT3.xml
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130 tools/effectiveT3/tool_dependencies.xml
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131
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132
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133 Licence (MIT)
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134 =============
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135
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136 Permission is hereby granted, free of charge, to any person obtaining a copy
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137 of this software and associated documentation files (the "Software"), to deal
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138 in the Software without restriction, including without limitation the rights
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139 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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140 copies of the Software, and to permit persons to whom the Software is
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141 furnished to do so, subject to the following conditions:
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142
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143 The above copyright notice and this permission notice shall be included in
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144 all copies or substantial portions of the Software.
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145
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146 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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147 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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148 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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149 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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150 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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151 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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152 THE SOFTWARE.
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153
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154 NOTE: This is the licence for the Galaxy Wrapper only.
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155 EffectiveT3 is available and licenced separately.