Mercurial > repos > peterjc > clinod
annotate tools/clinod/README.rst @ 3:6a9debe4b860 draft
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author | peterjc |
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date | Wed, 18 Sep 2013 06:09:33 -0400 |
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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 2011-2013 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 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 This NoD wrapper is available from the Galaxy Tool Shed at: |
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13 http://toolshed.g2.bx.psu.edu/view/peterjc/clinod |
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14 |
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15 |
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16 Automated Installation |
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17 ====================== |
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18 |
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19 This should be straightforward, Galaxy should automatically download and install |
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20 the JAR file for clinod v1.3 and the batchman executable from the Stuttgart |
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21 Neural Network Simulator (SNNS), and set the $CLINOD to their folder. |
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22 |
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23 |
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24 Manual Installation |
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25 =================== |
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26 This wrapper expects the java binary to be on the system PATH, and to be able |
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27 to access command line NoD as $CLINOD/clinod-1.3.jar which means if you used |
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28 /opt/clinod/clinod-1.3.jar set the environment variable $CLINOD to /opt/clinod |
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29 |
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30 Internally NoD calls the binary batchman v1.0 from the Stuttgart Neural Network |
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31 Simulator (SNNS) v4.2 or 4.3 software suite. This binary can either be on the |
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32 system path or located next to the JAR file, i.e. /opt/clinod/batchman |
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33 |
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34 To install the wrapper copy or move the following files under the Galaxy tools |
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35 folder, e.g. in a tools/clinod folder: |
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36 |
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37 * clinod.xml (the Galaxy tool definition) |
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38 * README.rst (this file) |
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39 |
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40 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the |
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41 tool. If you are using other protein analysis tools like TMHMM or SignalP, put |
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42 it next to them. Just add the line:: |
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43 |
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44 <tool file="clinod/clinod.xml" /> |
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45 |
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46 If you wish to run the unit tests, also add this to tools_conf.xml.sample |
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47 and move/copy the test-data files under Galaxy's test-data folder. Then:: |
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48 |
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49 $ ./run_functional_tests.sh -id clinod |
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50 |
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51 That's it. |
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52 |
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53 |
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54 History |
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55 ======= |
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56 |
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57 ======= ====================================================================== |
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58 Version Changes |
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59 ------- ---------------------------------------------------------------------- |
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60 v0.0.1 - Initial public release |
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61 v0.0.2 - Treat non-zero return codes as errors |
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62 v0.0.3 - Describe output table in help |
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63 v0.0.4 - Added unit test |
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64 v0.0.5 - Link to Tool Shed added to help text and this documentation. |
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65 - Automated tool installation. |
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66 v0.0.6 - Adopted standard MIT licence. |
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67 - Use reStructuredText for this README file. |
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68 - Updated citation information (Cock et al. 2013). |
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69 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy |
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70 ======= ====================================================================== |
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71 |
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72 |
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73 Developers |
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74 ========== |
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75 |
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76 This script and related tools were initially developed on the following hg branch: |
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77 http://bitbucket.org/peterjc/galaxy-central/src/tools |
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78 |
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79 Development has now moved to a dedicated GitHub repository: |
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80 https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod |
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81 |
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82 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use |
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83 the following command from the Galaxy root folder:: |
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84 |
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85 $ tar -czf clinod.tar.gz tools/clinod/README.rst tools/clinod/clinod.xml tools/clinod/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular |
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86 |
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87 Check this worked:: |
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88 |
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89 $ tar -tzf clinod.tar.gz |
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90 tools/clinod/README.rst |
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91 tools/clinod/clinod.xml |
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92 tools/clinod/tool_dependencies.xml |
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93 test-data/four_human_proteins.fasta |
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94 test-data/four_human_proteins.clinod-1.3.tabular |
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95 |
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96 |
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97 Licence (MIT) |
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98 ============= |
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99 |
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100 Permission is hereby granted, free of charge, to any person obtaining a copy |
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101 of this software and associated documentation files (the "Software"), to deal |
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102 in the Software without restriction, including without limitation the rights |
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103 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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104 copies of the Software, and to permit persons to whom the Software is |
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105 furnished to do so, subject to the following conditions: |
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106 |
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107 The above copyright notice and this permission notice shall be included in |
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108 all copies or substantial portions of the Software. |
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109 |
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110 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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111 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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112 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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113 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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114 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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115 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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116 THE SOFTWARE. |
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117 |
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118 NOTE: This is the licence for the Galaxy Wrapper only. Command line |
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119 NoD is available and licenced separately. |