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