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1 Galaxy wrapper for Command line NoD predictor (v1.3)
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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 Command line NoD predictor is a tool for predicting nucleolar localization
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9 sequences (NoLSs) in a FASTA file of proteins using a neural network. There
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10 is also a webtool version at http://www.compbio.dundee.ac.uk/www-nod/
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11
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12
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13 Installation
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14 ============
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15 This wrapper expects the java binary to be on the system PATH, and to be able
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16 to access command line NoD as /opt/clinod/clinod-1.3.jar (edit clinod.xml if
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17 you wish to use a different location).
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18
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19 Internally NoD calls the binary batchman from the Stuttgart Neural Network
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20 Simulator (SNNS) v 4.2 software suite. This binary can either be on the system
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21 path or located next to the JAR file, i.e. /opt/clinod/batchman
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22
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23 To install the wrapper copy or move the following files under the Galaxy tools
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24 folder, e.g. in a tools/protein_analysis folder:
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25
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26 * clinod.xml (the Galaxy tool definition)
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27 * clinod.txt (this README file)
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28
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29 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
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30 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
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31 it next to them. Just add the line:
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32
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33 <tool file="protein_analysis/clinod.xml" />
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34
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35 That's it.
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36
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37
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38 History
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39 =======
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40
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41 v0.0.1 - Initial public release
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42
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43
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44 Developers
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45 ==========
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46
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47 This script and related tools are being developed on the following hg branch:
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48 http://bitbucket.org/peterjc/galaxy-central/src/tools
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49
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50 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
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51 the following command from the Galaxy root folder:
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52
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53 $ tar -czf clinod.tar.gz tools/protein_analysis/clinod.xml tools/protein_analysis/clinod.txt
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54
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55 Check this worked:
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56
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57 $ tar -tzf clinod.tar.gz
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58 tools/protein_analysis/clinod.xml
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59 tools/protein_analysis/clinod.txt
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60
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61
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62 Licence (MIT/BSD style)
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63 =======================
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64
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65 Permission to use, copy, modify, and distribute this software and its
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66 documentation with or without modifications and for any purpose and
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67 without fee is hereby granted, provided that any copyright notices
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68 appear in all copies and that both those copyright notices and this
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69 permission notice appear in supporting documentation, and that the
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70 names of the contributors or copyright holders not be used in
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71 advertising or publicity pertaining to distribution of the software
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72 without specific prior permission.
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73
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74 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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75 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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76 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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77 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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78 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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79 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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80 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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81 OR PERFORMANCE OF THIS SOFTWARE.
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82
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83 NOTE: This is the licence for the Galaxy Wrapper only. Command line
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84 NoD is available and licenced separately.
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