Mercurial > repos > peterjc > clinod
annotate tools/clinod/README.rst @ 5:9485cdfca57e draft
v0.0.8 internal changes
author | peterjc |
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date | Wed, 05 Aug 2015 10:58:54 -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 |
5 | 4 This wrapper is copyright 2011-2015 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 |
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28 used ``/opt/clinod/clinod-1.3.jar`` set the environment variable ``$CLINOD`` |
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29 to ``/opt/clinod`` |
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30 |
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31 Internally NoD calls the binary batchman v1.0 from the Stuttgart Neural Network |
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32 Simulator (SNNS) v4.2 or 4.3 software suite. This binary can either be on the |
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33 system path or located next to the JAR file, i.e. ``/opt/clinod/batchman`` |
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34 |
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35 To install the wrapper copy or move the following files under the Galaxy tools |
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36 folder, e.g. in a ``tools/clinod`` folder: |
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37 |
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38 * ``clinod.xml`` (the Galaxy tool definition) |
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39 * ``README.rst`` (this file) |
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40 |
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41 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the |
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42 tool. If you are using other protein analysis tools like TMHMM or SignalP, put |
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43 it next to them. Just add the line:: |
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44 |
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45 <tool file="clinod/clinod.xml" /> |
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46 |
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47 If you wish to run the unit tests, also move/copy the ``test-data/`` files |
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48 under Galaxy's ``test-data/`` folder. Then:: |
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49 |
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50 $ ./run_tests.sh -id clinod |
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51 |
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52 That's it. |
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53 |
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54 |
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55 History |
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56 ======= |
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57 |
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58 ======= ====================================================================== |
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59 Version Changes |
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60 ------- ---------------------------------------------------------------------- |
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61 v0.0.1 - Initial public release |
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62 v0.0.2 - Treat non-zero return codes as errors |
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63 v0.0.3 - Describe output table in help |
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64 v0.0.4 - Added unit test |
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65 v0.0.5 - Link to Tool Shed added to help text and this documentation. |
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66 - Automated tool installation. |
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67 v0.0.6 - Adopted standard MIT licence. |
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68 - Use reStructuredText for this README file. |
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69 - Updated citation information (Cock et al. 2013). |
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70 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy |
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71 v0.0.7 - Use the new ``$GALAXY_SLOTS`` environment variable for thread count. |
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72 - Tool definition now embeds citation information. |
5 | 73 v0.0.8 - Reorder XML elements (internal change only). |
74 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). | |
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75 ======= ====================================================================== |
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76 |
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77 |
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78 Developers |
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79 ========== |
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80 |
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81 This script and related tools were initially developed on the following hg branch: |
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82 http://bitbucket.org/peterjc/galaxy-central/src/tools |
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83 |
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84 Development has now moved to a dedicated GitHub repository: |
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85 https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod |
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86 |
5 | 87 For pushing a release to the test or main "Galaxy Tool Shed", use the following |
88 Planemo commands (which requires you have set your Tool Shed access details in | |
89 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: | |
90 | |
91 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clinod/ | |
92 ... | |
93 | |
94 or:: | |
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95 |
5 | 96 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/clinod/ |
97 ... | |
98 | |
99 To just build and check the tar ball, use:: | |
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100 |
5 | 101 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/clinod/ |
102 ... | |
103 $ tar -tzf shed_upload.tar.gz | |
104 test-data/four_human_proteins.fasta | |
105 test-data/four_human_proteins.clinod-1.3.tabular | |
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106 tools/clinod/README.rst |
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107 tools/clinod/clinod.xml |
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108 tools/clinod/tool_dependencies.xml |
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109 |
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110 |
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111 Licence (MIT) |
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112 ============= |
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113 |
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114 Permission is hereby granted, free of charge, to any person obtaining a copy |
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115 of this software and associated documentation files (the "Software"), to deal |
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116 in the Software without restriction, including without limitation the rights |
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117 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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118 copies of the Software, and to permit persons to whom the Software is |
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119 furnished to do so, subject to the following conditions: |
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120 |
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121 The above copyright notice and this permission notice shall be included in |
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122 all copies or substantial portions of the Software. |
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123 |
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124 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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125 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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126 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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127 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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128 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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129 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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130 THE SOFTWARE. |
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131 |
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132 NOTE: This is the licence for the Galaxy Wrapper only. Command line |
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133 NoD is available and licenced separately. |