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annotate tools/protein_analysis/nlstradamus.txt @ 0:0ad90e5eb390

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Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 17:39:58 -0400
parents
children f93ad4882338
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0ad90e5eb390 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
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1 Galaxy wrapper for NLStradamus v1.7 (C++ version)
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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 NLStradamus is a command line tools for predicting nuclear localization
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9 signals (NLSs) in a FASTA file of proteins using a Hidden Markov Model (HMM).
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10
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11 A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses.
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12 NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction.
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13 BMC Bioinformatics. 2009 Jun 29;10(1):202.
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14
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15 http://www.moseslab.csb.utoronto.ca/NLStradamus
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16
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17 Early versions of NLStradamus did not have a native tabular output format, this
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18 was added in version 1.7. Additionally a fast C++ implementation was added at
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19 this point (early versions of NLStradamus came as a perl script only). This
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20 wrapper expects the compiled C++ binary "NLStradamus" to be on the system PATH.
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21
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22 To install the wrapper installed the following files under the Galaxy tools
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23 folder, e.g. in a tools/protein_analysis folder:
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24
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25 * nlstradamus.xml (the Galaxy tool definition)
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26 * nlstradamus.txt (this README file)
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27
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28 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
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29 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
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30 it next to them. Just add the line:
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31
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32 <tool file="protein_analysis/nlstradamus.xml" />
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33
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34 That's it.
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35
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36
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37 History
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38 =======
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39
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40 v0.0.3 - Initial public release
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42
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43 Developers
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44 ==========
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45
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46 This script and related tools are being developed on the following hg branch:
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47 http://bitbucket.org/peterjc/galaxy-central/src/tools
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48
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49 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
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50 the following command from the Galaxy root folder:
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51
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52 tar -czf nlstradmus.tar.gz tools/protein_analysis/nlstradum.xml tools/protein_analysis/nlstradum.txt
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53
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54 Check this worked:
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55
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56 $ tar -tzf nlstradmus.tar.gz
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57 filter/seq_filter_by_id.py
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58 filter/seq_filter_by_id.txt
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59 filter/seq_filter_by_id.xml
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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. NLStradamus
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84 is available and licenced separately.