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Uploaded v0.0.7 with automatic installation of the C++ binary.
author peterjc
date Tue, 23 Apr 2013 11:59:14 -0400
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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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3
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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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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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15
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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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26 Automated Installation
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27 ======================
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28
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29 This should be straightforward, Galaxy should automatically download and install
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30 the C++ implementation of NLStradamus v1.8, and run the unit tests.
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33 Manual Installation
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34 ===================
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35 This wrapper expects the compiled C++ binary "NLStradamus" to be on the system
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36 PATH.
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37
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38 To install the wrapper copy or move the following files under the Galaxy tools
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39 folder, e.g. in a tools/protein_analysis folder:
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40
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41 * nlstradamus.xml (the Galaxy tool definition)
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42 * nlstradamus.txt (this README file)
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43
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44 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
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45 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
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46 it next to them. Just add the line (matching the chosen install path):
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47
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48 <tool file="protein_analysis/nlstradamus.xml" />
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49
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50 If you wish to run the unit tests, also add this to tools_conf.xml.sample
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51 and move/copy the test-data files under Galaxy's test-data folder. Then:
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52
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53 $ ./run_functional_tests.sh -id nlstradamus
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54
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55 That's it.
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56
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57
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58 History
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59 =======
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60
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61 v0.0.3 - Initial public release
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62 v0.0.4 - Adding DOI link to reference
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63 (Documentation change only)
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64 v0.0.5 - Assume non-zero return codes are errors
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65 v0.0.6 - Show output help text using a table
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66 - Added unit tests
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67 v0.0.7 - Automatic installation of the NLStradamus binary when installed
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68 via the Galaxy Tool Shed
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69
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70
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71 Developers
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72 ==========
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73
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74 This script and related tools are being developed on the following hg branch:
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75 http://bitbucket.org/peterjc/galaxy-central/src/tools
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76
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77 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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78 the following command from the Galaxy root folder:
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79
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80 $ tar -czf nlstradmus.tar.gz tools/nlstradamus/nlstradamus.xml tools/nlstradamus/nlstradamus.txt tools/nlstradamus/tool_dependencies.xml 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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81
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82 Check this worked:
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83
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84 $ tar -tzf nlstradmus.tar.gz
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85 tools/nlstradamus/nlstradamus.xml
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86 tools/nlstradamus/nlstradamus.txt
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87 tools/nlstradamus/tool_dependencies.xml
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88 test-data/four_human_proteins.fasta
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89 test-data/four_human_proteins.nlstradamus.tabular
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90 test-data/empty.fasta
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91 test-data/empty_nlstradamus.tabular
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92
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93
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94 Licence (MIT/BSD style)
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95 =======================
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96
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97 Permission to use, copy, modify, and distribute this software and its
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98 documentation with or without modifications and for any purpose and
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99 without fee is hereby granted, provided that any copyright notices
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100 appear in all copies and that both those copyright notices and this
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101 permission notice appear in supporting documentation, and that the
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102 names of the contributors or copyright holders not be used in
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103 advertising or publicity pertaining to distribution of the software
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104 without specific prior permission.
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105
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106 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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107 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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108 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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109 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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110 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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111 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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112 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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113 OR PERFORMANCE OF THIS SOFTWARE.
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114
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115 NOTE: This is the licence for the Galaxy Wrapper only. NLStradamus
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116 is is available and licenced separately (under the GPL v3 or later).