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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
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children 1ea715da1879
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3:b0b927299aee 4:f7ce32e13bc6
1 Galaxy wrapper for EffectiveT3 v1.0.1
2 =====================================
3
4 This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below.
7
8 This is a wrapper for the command line Java tool EffectiveT3, v1.0.1,
9
10 Jehl, Arnold and Rattei.
11 Effective - a database of predicted secreted bacterial proteins
12 Nucleic Acids Research, 39(Database issue), D591-5, 2011.
13 http://dx.doi.org/10.1093/nar/gkq1154
14
15 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei.
16 Sequence-based prediction of type III secreted proteins.
17 PLoS Pathog. 5(4):e1000376, 2009.
18 http://dx.doi.org/10.1371/journal.ppat.1000376
19
20 http://effectors.org/
21
22 This wrapper is available from the Galaxy Tool Shed at:
23 http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
24
25
26 Automated Installation
27 ======================
28
29 This should be straightforward, Galaxy should automatically download and install
30 the Jar files for effectiveT3 v1.0.1 and the three models (animal, plant and std).
31
32
33 Manual Installation
34 ===================
35
36 You can change the path by setting the environment variable EFFECTIVET3 to the
37 relevant folder, but by default it expects the following files to be installed
38 at these locations::
39
40 /opt/EffectiveT3/TTSS_GUI-1.0.1.jar
41 /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar
42 /opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar
43 /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar
44
45 To install the wrapper copy or move the following files under the Galaxy tools
46 folder, e.g. in a tools/effectiveT3 folder:
47
48 * effectiveT3.xml (the Galaxy tool definition)
49 * effectiveT3.py (the Python wrapper script)
50 * README.rst (this file)
51
52 Also copy effectiveT3.loc.sample to effectiveT3.loc in the tool-data folder
53 (and edit if appropriate, e.g. to add or remove a model).
54
55 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
56 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
57 it next to them. Just add the line::
58
59 <tool file="effectiveT3/effectiveT3.xml" />
60
61 If you wish to run the unit tests, also add this to tools_conf.xml.sample
62 and move/copy the test-data files under Galaxy's test-data folder. Then::
63
64 $ ./run_functional_tests.sh -id effectiveT3
65
66 That's it.
67
68
69 History
70 =======
71
72 ======= ======================================================================
73 Version Changes
74 ------- ----------------------------------------------------------------------
75 v0.0.7 - Initial public release
76 v0.0.8 - Include effectiveT3.loc.sample in Tool Shed
77 v0.0.9 - Check the return code for errors in the XML
78 v0.0.10 - Added unit test
79 v0.0.11 - Automated installation
80 - Record version of Python script when called from Galaxy
81 - Link to Tool Shed added to help text and this documentation.
82 v0.0.12 - More explicit naming of the output dataset.
83 - Adopt standard MIT licence.
84 - Use reStructuredText for this README file.
85 - Updated citation information (Cock et al. 2013).
86 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
87 ======= ======================================================================
88
89
90 Developers
91 ==========
92
93 This script and related tools were initially developed on the following hg branch:
94 http://bitbucket.org/peterjc/galaxy-central/src/tools
95
96 Development has now moved to a dedicated GitHub repository:
97 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
98
99 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
100 the following command from the Galaxy root folder::
101
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
103
104
105 Check this worked::
106
107 $ tar -tzf effectiveT3.tar.gz
108 tools/effectiveT3/README.rst
109 tools/effectiveT3/effectiveT3.xml
110 tools/effectiveT3/effectiveT3.py
111 tools/effectiveT3/tool_dependencies.xml
112 tool-data/effectiveT3.loc.sample
113 test-data/four_human_proteins.fasta
114 test-data/four_human_proteins.effectiveT3.tabular
115 test-data/empty.fasta
116 test-data/empty_effectiveT3.tabular
117
118
119 Licence (MIT)
120 =============
121
122 Permission is hereby granted, free of charge, to any person obtaining a copy
123 of this software and associated documentation files (the "Software"), to deal
124 in the Software without restriction, including without limitation the rights
125 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
126 copies of the Software, and to permit persons to whom the Software is
127 furnished to do so, subject to the following conditions:
128
129 The above copyright notice and this permission notice shall be included in
130 all copies or substantial portions of the Software.
131
132 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
133 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
134 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
135 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
136 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
137 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
138 THE SOFTWARE.
139
140 NOTE: This is the licence for the Galaxy Wrapper only.
141 EffectiveT3 is available and licenced separately.