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comparison tools/effectiveT3/effectiveT3.txt @ 2:66e9d4c44ca2 draft

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Uploaded v0.0.11, auto installation
author peterjc
date Tue, 30 Apr 2013 09:32:56 -0400
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1:7479dbb285b5 2:66e9d4c44ca2
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
23 Automated Installation
24 ======================
25
26 This should be straightforward, Galaxy should automatically download and install
27 the Jar files for effectiveT3 v1.0.1 and the three models (animal, plant and std).
28
29
30 Manual Installation
31 ===================
32
33 You can change the path by setting the environment variable EFFECTIVET3 to the
34 relevant folder, but by default it expects the following files to be installed
35 at these locations:
36
37 /opt/EffectiveT3/TTSS_GUI-1.0.1.jar
38 /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar
39 /opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar
40 /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar
41
42 To install the wrapper copy or move the following files under the Galaxy tools
43 folder, e.g. in a tools/effectiveT3 folder:
44
45 * effectiveT3.xml (the Galaxy tool definition)
46 * effectiveT3.py (the Python wrapper script)
47 * effectiveT3.txt (this README file)
48
49 Also copy effectiveT3.loc.sample to effectiveT3.loc in the tool-data folder
50 (and edit if appropriate, e.g. to add or remove a model).
51
52 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
53 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
54 it next to them. Just add the line:
55
56 <tool file="effectiveT3/effectiveT3.xml" />
57
58 If you wish to run the unit tests, also add this to tools_conf.xml.sample
59 and move/copy the test-data files under Galaxy's test-data folder.
60
61 $ ./run_functional_tests.sh -id effectiveT3
62
63 That's it.
64
65
66 History
67 =======
68
69 v0.0.7 - Initial public release
70 v0.0.8 - Include effectiveT3.loc.sample in Tool Shed
71 v0.0.9 - Check the return code for errors in the XML
72 v0.0.10- Added unit test
73 v0.0.11- Automated installation
74 - Record version of Python script when called from Galaxy
75
76
77 Developers
78 ==========
79
80 This script and related tools are being developed on the following hg branch:
81 http://bitbucket.org/peterjc/galaxy-central/src/tools
82
83 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
84 the following command from the Galaxy root folder:
85
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
87
88
89 Check this worked:
90
91 $ tar -tzf effectiveT3.tar.gz
92 tools/effectiveT3/effectiveT3.xml
93 tools/effectiveT3/effectiveT3.py
94 tools/effectiveT3/effectiveT3.txt
95 tools/effectiveT3/tool_dependencies.xml
96 tool-data/effectiveT3.loc.sample
97 test-data/four_human_proteins.fasta
98 test-data/four_human_proteins.effectiveT3.tabular
99 test-data/empty.fasta
100 test-data/empty_effectiveT3.tabular
101
102
103 Licence (MIT/BSD style)
104 =======================
105
106 Permission to use, copy, modify, and distribute this software and its
107 documentation with or without modifications and for any purpose and
108 without fee is hereby granted, provided that any copyright notices
109 appear in all copies and that both those copyright notices and this
110 permission notice appear in supporting documentation, and that the
111 names of the contributors or copyright holders not be used in
112 advertising or publicity pertaining to distribution of the software
113 without specific prior permission.
114
115 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
116 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
117 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
118 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
119 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
120 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
121 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
122 OR PERFORMANCE OF THIS SOFTWARE.
123
124 NOTE: This is the licence for the Galaxy Wrapper only.
125 EffectiveT3 is available and licenced separately.