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annotate tools/effectiveT3/README.rst @ 4:f7ce32e13bc6 draft

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Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
author peterjc
date Wed, 18 Sep 2013 06:11:36 -0400
parents
children 1ea715da1879
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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 2011-2013 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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14
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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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21
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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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28
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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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32
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33 Manual Installation
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34 ===================
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35
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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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39
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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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44
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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 folder
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53 (and edit if appropriate, e.g. to add or remove a model).
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54
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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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58
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59 <tool file="effectiveT3/effectiveT3.xml" />
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60
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61 If you wish to run the unit tests, also add this to tools_conf.xml.sample
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62 and move/copy the test-data files under Galaxy's test-data folder. Then::
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63
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64 $ ./run_functional_tests.sh -id effectiveT3
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65
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66 That's it.
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67
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68
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69 History
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70 =======
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71
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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 ======= ======================================================================
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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 script and related tools were initially developed on the following hg branch:
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94 http://bitbucket.org/peterjc/galaxy-central/src/tools
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95
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96 Development has now moved to a dedicated GitHub repository:
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97 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
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98
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99 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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100 the following command from the Galaxy root folder::
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101
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102 $ tar -czf effectiveT3.tar.gz tools/effectiveT3/README.rst tools/effectiveT3/effectiveT3.xml tools/effectiveT3/effectiveT3.py tools/effectiveT3/tool_dependencies.xml tool-data/effectiveT3.loc.sample test-data/four_human_proteins.fasta test-data/four_human_proteins.effectiveT3.tabular test-data/empty.fasta test-data/empty_effectiveT3.tabular
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103
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104
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105 Check this worked::
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106
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107 $ tar -tzf effectiveT3.tar.gz
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108 tools/effectiveT3/README.rst
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109 tools/effectiveT3/effectiveT3.xml
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110 tools/effectiveT3/effectiveT3.py
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111 tools/effectiveT3/tool_dependencies.xml
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112 tool-data/effectiveT3.loc.sample
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113 test-data/four_human_proteins.fasta
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114 test-data/four_human_proteins.effectiveT3.tabular
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115 test-data/empty.fasta
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116 test-data/empty_effectiveT3.tabular
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117
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118
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119 Licence (MIT)
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120 =============
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121
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122 Permission is hereby granted, free of charge, to any person obtaining a copy
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123 of this software and associated documentation files (the "Software"), to deal
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124 in the Software without restriction, including without limitation the rights
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125 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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126 copies of the Software, and to permit persons to whom the Software is
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127 furnished to do so, subject to the following conditions:
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128
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129 The above copyright notice and this permission notice shall be included in
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130 all copies or substantial portions of the Software.
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131
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132 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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133 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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134 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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135 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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136 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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137 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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138 THE SOFTWARE.
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139
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140 NOTE: This is the licence for the Galaxy Wrapper only.
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141 EffectiveT3 is available and licenced separately.