Mercurial > repos > peterjc > effectivet3
comparison tools/protein_analysis/effectiveT3.txt @ 0:43436379876f
Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:21:30 -0400 |
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children | e607c342312f |
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1 Galaxy wrapper for EffectiveT3 v1.0.1 | |
2 ===================================== | |
3 | |
4 This wrapper is copyright 2011 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 You can change the path by editing the definition near the start of the Python | |
23 script effectiveT3.py, but by default it expects the following files to be | |
24 installed at these locations: | |
25 | |
26 /opt/EffectiveT3/TTSS_GUI-1.0.1.jar | |
27 /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar | |
28 /opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar | |
29 /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar | |
30 | |
31 To install the wrapper copy or move the following files under the Galaxy tools | |
32 folder, e.g. in a tools/protein_analysis folder: | |
33 | |
34 * effectiveT3.xml (the Galaxy tool definition) | |
35 * effectiveT3.py (the Python wrapper script) | |
36 * effectiveT3.txt (this README file) | |
37 | |
38 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the | |
39 tool. If you are using other protein analysis tools like TMHMM or SignalP, put | |
40 it next to them. Just add the line: | |
41 | |
42 <tool file="protein_analysis/effectiveT3.xml" /> | |
43 | |
44 That's it. | |
45 | |
46 | |
47 History | |
48 ======= | |
49 | |
50 v0.0.7 - Initial public release | |
51 | |
52 | |
53 Developers | |
54 ========== | |
55 | |
56 This script and related tools are being developed on the following hg branch: | |
57 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
58 | |
59 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use | |
60 the following command from the Galaxy root folder: | |
61 | |
62 $ tar -czf effectiveT3.tar.gz tools/protein_analysis/effectiveT3.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt | |
63 | |
64 Check this worked: | |
65 | |
66 $ tar -tzf effectiveT3.tar.gz | |
67 tools/protein_analysis/effectiveT3.xml | |
68 tools/protein_analysis/effectiveT3.py | |
69 tools/protein_analysis/effectiveT3.txt | |
70 | |
71 | |
72 Licence (MIT/BSD style) | |
73 ======================= | |
74 | |
75 Permission to use, copy, modify, and distribute this software and its | |
76 documentation with or without modifications and for any purpose and | |
77 without fee is hereby granted, provided that any copyright notices | |
78 appear in all copies and that both those copyright notices and this | |
79 permission notice appear in supporting documentation, and that the | |
80 names of the contributors or copyright holders not be used in | |
81 advertising or publicity pertaining to distribution of the software | |
82 without specific prior permission. | |
83 | |
84 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
85 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
86 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
87 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
88 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
89 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
90 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
91 OR PERFORMANCE OF THIS SOFTWARE. | |
92 | |
93 NOTE: This is the licence for the Galaxy Wrapper only. NLStradamus | |
94 is available and licenced separately. |