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annotate tools/protein_analysis/nlstradamus.txt @ 1:f93ad4882338 draft

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Uploaded v0.0.6, adds unit tests and minor documentation changes.
author peterjc
date Wed, 17 Apr 2013 08:26:25 -0400
parents 0ad90e5eb390
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1 Galaxy wrapper for NLStradamus v1.7 or v1.8 (C++ version)
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2 =========================================================
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4 This wrapper is copyright 2011-2013 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 http://dx.doi.org/10.1186/1471-2105-10-202
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16 http://www.moseslab.csb.utoronto.ca/NLStradamus
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17
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18 Early versions of NLStradamus did not have a native tabular output format, this
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19 was added in version 1.7. Additionally a fast C++ implementation was added at
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20 this point (early versions of NLStradamus came as a perl script only).
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21
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22 Version 1.8 fixed a C++ compilation issue on modern compilers, but is otherwise
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23 unchanged.
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f93ad4882338 Uploaded v0.0.6, adds unit tests and minor documentation changes.
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26 Installation
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27 ============
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28 This wrapper expects the compiled C++ binary "NLStradamus" to be on the system
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29 PATH.
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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 * nlstradamus.xml (the Galaxy tool definition)
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35 * nlstradamus.txt (this README file)
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36
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37 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
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38 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
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39 it next to them. Just add the line:
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40
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41 <tool file="protein_analysis/nlstradamus.xml" />
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42
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43 If you wish to run the unit tests, also add this to tools_conf.xml.sample
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44 and move/copy the test-data files under Galaxy's test-data folder.
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45
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46 That's it.
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48
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49 History
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50 =======
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51
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52 v0.0.3 - Initial public release
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53 v0.0.4 - Adding DOI link to reference
f93ad4882338 Uploaded v0.0.6, adds unit tests and minor documentation changes.
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54 (Documentation change only)
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55 v0.0.5 - Assume non-zero return codes are errors
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56 v0.0.6 - Show output help text using a table
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57 - Added unit tests
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60 Developers
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61 ==========
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62
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63 This script and related tools are being developed on the following hg branch:
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64 http://bitbucket.org/peterjc/galaxy-central/src/tools
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65
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66 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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67 the following command from the Galaxy root folder:
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68
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69 $ tar -czf nlstradmus.tar.gz tools/protein_analysis/nlstradamus.xml tools/protein_analysis/nlstradamus.txt test-data/four_human_proteins.fasta test-data/four_human_proteins.nlstradamus.tabular test-data/empty.fasta test-data/empty_nlstradamus.tabular
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71 Check this worked:
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72
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73 $ tar -tzf nlstradmus.tar.gz
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74 tools/protein_analysis/nlstradamus.xml
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75 tools/protein_analysis/nlstradamus.txt
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76 test-data/four_human_proteins.fasta
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77 test-data/four_human_proteins.nlstradamus.tabular
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78 test-data/empty.fasta
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79 test-data/empty_nlstradamus.tabular
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81
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82 Licence (MIT/BSD style)
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83 =======================
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84
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85 Permission to use, copy, modify, and distribute this software and its
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86 documentation with or without modifications and for any purpose and
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87 without fee is hereby granted, provided that any copyright notices
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88 appear in all copies and that both those copyright notices and this
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89 permission notice appear in supporting documentation, and that the
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90 names of the contributors or copyright holders not be used in
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91 advertising or publicity pertaining to distribution of the software
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92 without specific prior permission.
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93
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94 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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95 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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96 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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97 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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98 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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99 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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100 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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101 OR PERFORMANCE OF THIS SOFTWARE.
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102
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103 NOTE: This is the licence for the Galaxy Wrapper only. NLStradamus
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104 is available and licenced separately.