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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
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23 Automated Installation
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24 ======================
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25
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26 This should be straightforward, Galaxy should automatically download and install
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27 the Jar files for effectiveT3 v1.0.1 and the three models (animal, plant and std).
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28
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29
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30 Manual Installation
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31 ===================
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32
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33 You can change the path by setting the environment variable EFFECTIVET3 to the
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34 relevant folder, but by default it expects the following files to be installed
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35 at these locations:
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36
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37 /opt/EffectiveT3/TTSS_GUI-1.0.1.jar
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38 /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar
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39 /opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar
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40 /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar
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41
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42 To install the wrapper copy or move the following files under the Galaxy tools
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43 folder, e.g. in a tools/effectiveT3 folder:
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44
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45 * effectiveT3.xml (the Galaxy tool definition)
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46 * effectiveT3.py (the Python wrapper script)
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47 * effectiveT3.txt (this README file)
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48
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49 Also copy effectiveT3.loc.sample to effectiveT3.loc in the tool-data folder
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50 (and edit if appropriate, e.g. to add or remove a model).
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51
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52 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
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53 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
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54 it next to them. Just add the line:
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55
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56 <tool file="effectiveT3/effectiveT3.xml" />
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57
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58 If you wish to run the unit tests, also add this to tools_conf.xml.sample
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59 and move/copy the test-data files under Galaxy's test-data folder.
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60
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61 $ ./run_functional_tests.sh -id effectiveT3
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62
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63 That's it.
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64
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65
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66 History
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67 =======
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68
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69 v0.0.7 - Initial public release
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70 v0.0.8 - Include effectiveT3.loc.sample in Tool Shed
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71 v0.0.9 - Check the return code for errors in the XML
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72 v0.0.10- Added unit test
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73 v0.0.11- Automated installation
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74 - Record version of Python script when called from Galaxy
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75
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76
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77 Developers
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78 ==========
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79
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80 This script and related tools are being developed on the following hg branch:
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81 http://bitbucket.org/peterjc/galaxy-central/src/tools
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82
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83 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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84 the following command from the Galaxy root folder:
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85
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86 $ tar -czf effectiveT3.tar.gz tools/effectiveT3/effectiveT3.xml tools/effectiveT3/effectiveT3.py tools/effectiveT3/effectiveT3.txt 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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87
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88
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89 Check this worked:
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90
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91 $ tar -tzf effectiveT3.tar.gz
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92 tools/effectiveT3/effectiveT3.xml
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93 tools/effectiveT3/effectiveT3.py
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94 tools/effectiveT3/effectiveT3.txt
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95 tools/effectiveT3/tool_dependencies.xml
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96 tool-data/effectiveT3.loc.sample
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97 test-data/four_human_proteins.fasta
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98 test-data/four_human_proteins.effectiveT3.tabular
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99 test-data/empty.fasta
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100 test-data/empty_effectiveT3.tabular
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101
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102
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103 Licence (MIT/BSD style)
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104 =======================
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105
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106 Permission to use, copy, modify, and distribute this software and its
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107 documentation with or without modifications and for any purpose and
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108 without fee is hereby granted, provided that any copyright notices
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109 appear in all copies and that both those copyright notices and this
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110 permission notice appear in supporting documentation, and that the
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111 names of the contributors or copyright holders not be used in
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112 advertising or publicity pertaining to distribution of the software
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113 without specific prior permission.
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114
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115 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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116 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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117 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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118 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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119 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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120 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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121 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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122 OR PERFORMANCE OF THIS SOFTWARE.
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123
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124 NOTE: This is the licence for the Galaxy Wrapper only.
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125 EffectiveT3 is available and licenced separately.
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