Mercurial > repos > peterjc > nlstradamus
annotate tools/nlstradamus/README.rst @ 3:b2e648e55ed7 draft
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author | peterjc |
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date | Wed, 18 Sep 2013 06:15:33 -0400 |
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3
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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 (MIT licence). |
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7 |
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8 NLStradamus is a command line tool 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 This wrapper is available from the Galaxy Tool Shed at: |
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12 http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus |
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13 |
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14 A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses. |
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15 NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. |
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16 BMC Bioinformatics. 2009 Jun 29;10(1):202. |
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17 http://dx.doi.org/10.1186/1471-2105-10-202 |
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18 |
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19 http://www.moseslab.csb.utoronto.ca/NLStradamus |
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20 |
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21 Early versions of NLStradamus did not have a native tabular output format, this |
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22 was added in version 1.7. Additionally a fast C++ implementation was added at |
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23 this point (early versions of NLStradamus came as a perl script only). |
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24 |
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25 Version 1.8 fixed a C++ compilation issue on modern compilers, but is otherwise |
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26 unchanged. |
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27 |
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28 |
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29 Automated Installation |
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30 ====================== |
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31 |
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32 This should be straightforward, Galaxy should automatically download and install |
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33 the C++ implementation of NLStradamus v1.8, and run the unit tests. |
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34 |
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35 |
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36 Manual Installation |
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37 =================== |
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38 This wrapper expects the compiled C++ binary "NLStradamus" to be on the system |
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39 PATH. |
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40 |
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41 To install the wrapper copy or move the following files under the Galaxy tools |
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42 folder, e.g. in a tools/protein_analysis folder: |
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43 |
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44 * nlstradamus.xml (the Galaxy tool definition) |
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45 * nlstradamus.txt (this README file) |
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46 |
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47 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the |
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48 tool. If you are using other protein analysis tools like TMHMM or SignalP, put |
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49 it next to them. Just add the line (matching the chosen install path):: |
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50 |
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51 <tool file="protein_analysis/nlstradamus.xml" /> |
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52 |
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53 If you wish to run the unit tests, also add this to tools_conf.xml.sample |
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54 and move/copy the test-data files under Galaxy's test-data folder. Then:: |
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55 |
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56 $ ./run_functional_tests.sh -id nlstradamus |
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57 |
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58 That's it. |
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59 |
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60 |
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61 History |
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62 ======= |
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63 |
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64 ======= ====================================================================== |
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65 Version Changes |
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66 ------- ---------------------------------------------------------------------- |
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67 v0.0.3 - Initial public release |
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68 v0.0.4 - Adding DOI link to reference |
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69 (Documentation change only) |
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70 v0.0.5 - Assume non-zero return codes are errors |
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71 v0.0.6 - Show output help text using a table |
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72 - Added unit tests |
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73 v0.0.7 - Automatic installation of the NLStradamus binary when installed |
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74 via the Galaxy Tool Shed |
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75 v0.0.8 - Link to Tool Shed added to help text and this documentation. |
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76 - Use reStructuredText for this README file. |
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77 - Adopted standard MIT licence. |
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78 - Updated citation information (Cock et al. 2013). |
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79 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy |
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80 ======= ====================================================================== |
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81 |
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82 |
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83 Developers |
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84 ========== |
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85 |
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86 This script and related tools are being developed on the following hg branch: |
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87 http://bitbucket.org/peterjc/galaxy-central/src/tools |
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88 |
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89 Development has now moved to a dedicated GitHub repository: |
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90 https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus |
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91 |
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92 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use |
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93 the following command from the Galaxy root folder:: |
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94 |
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95 $ tar -czf nlstradmus.tar.gz tools/nlstradamus/README.rst tools/nlstradamus/nlstradamus.xml 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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96 |
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97 Check this worked:: |
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98 |
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99 $ tar -tzf nlstradmus.tar.gz |
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100 tools/nlstradamus/README.rst |
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101 tools/nlstradamus/nlstradamus.xml |
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102 tools/nlstradamus/tool_dependencies.xml |
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103 test-data/four_human_proteins.fasta |
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104 test-data/four_human_proteins.nlstradamus.tabular |
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105 test-data/empty.fasta |
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106 test-data/empty_nlstradamus.tabular |
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107 |
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108 |
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109 Licence (MIT) |
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110 ============= |
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111 |
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112 Permission is hereby granted, free of charge, to any person obtaining a copy |
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113 of this software and associated documentation files (the "Software"), to deal |
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114 in the Software without restriction, including without limitation the rights |
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115 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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116 copies of the Software, and to permit persons to whom the Software is |
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117 furnished to do so, subject to the following conditions: |
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118 |
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119 The above copyright notice and this permission notice shall be included in |
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120 all copies or substantial portions of the Software. |
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121 |
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122 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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123 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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124 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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125 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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126 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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127 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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128 THE SOFTWARE. |