Mercurial > repos > peterjc > effectivet3
annotate tools/protein_analysis/effectiveT3.txt @ 1:e607c342312f
Wrapper v0.0.8, includes effectiveT3.loc.sample file
author | peterjc |
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date | Tue, 02 Aug 2011 07:06:13 -0400 |
parents | 43436379876f |
children | 5a8e09f115f8 |
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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 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 |
1 | 22 |
23 Installation | |
24 =========== | |
25 | |
0
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26 You can change the path by editing the definition near the start of the Python |
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27 script effectiveT3.py, but by default it expects the following files to be |
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28 installed at these locations: |
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29 |
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30 /opt/EffectiveT3/TTSS_GUI-1.0.1.jar |
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31 /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar |
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32 /opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar |
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33 /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar |
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34 |
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35 To install the wrapper copy or move the following files under the Galaxy tools |
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36 folder, e.g. in a tools/protein_analysis folder: |
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37 |
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38 * effectiveT3.xml (the Galaxy tool definition) |
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39 * effectiveT3.py (the Python wrapper script) |
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40 * effectiveT3.txt (this README file) |
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41 |
1 | 42 Also copy effectiveT3.loc.sample to effectiveT3.loc in the tool-data folder |
43 (and edit if appropriate, e.g. to add or remove a model). | |
44 | |
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45 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the |
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46 tool. If you are using other protein analysis tools like TMHMM or SignalP, put |
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47 it next to them. Just add the line: |
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48 |
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49 <tool file="protein_analysis/effectiveT3.xml" /> |
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50 |
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51 That's it. |
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52 |
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53 |
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54 History |
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55 ======= |
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56 |
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57 v0.0.7 - Initial public release |
1 | 58 v0.0.8 - Include effectiveT3.loc.sample in Tool Shed |
0
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59 |
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60 |
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61 Developers |
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62 ========== |
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63 |
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64 This script and related tools are being developed on the following hg branch: |
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65 http://bitbucket.org/peterjc/galaxy-central/src/tools |
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66 |
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67 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use |
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68 the following command from the Galaxy root folder: |
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69 |
1 | 70 $ tar -czf effectiveT3.tar.gz tools/protein_analysis/effectiveT3.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt tool-data/effectiveT3.loc.sample |
0
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71 |
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72 Check this worked: |
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73 |
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74 $ tar -tzf effectiveT3.tar.gz |
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75 tools/protein_analysis/effectiveT3.xml |
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76 tools/protein_analysis/effectiveT3.py |
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77 tools/protein_analysis/effectiveT3.txt |
1 | 78 tool-data/effectiveT3.loc.sample |
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79 |
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80 Licence (MIT/BSD style) |
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81 ======================= |
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82 |
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83 Permission to use, copy, modify, and distribute this software and its |
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84 documentation with or without modifications and for any purpose and |
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85 without fee is hereby granted, provided that any copyright notices |
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86 appear in all copies and that both those copyright notices and this |
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87 permission notice appear in supporting documentation, and that the |
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88 names of the contributors or copyright holders not be used in |
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89 advertising or publicity pertaining to distribution of the software |
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90 without specific prior permission. |
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91 |
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92 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL |
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93 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED |
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94 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE |
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95 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT |
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96 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS |
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97 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE |
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98 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE |
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99 OR PERFORMANCE OF THIS SOFTWARE. |
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100 |
1 | 101 NOTE: This is the licence for the Galaxy Wrapper only. |
102 EffectiveT3 is available and licenced separately. |